From 0966335cdd192e391fef56023cfe5a587c16f8dc Mon Sep 17 00:00:00 2001
From: Karl5766 <Karl5766@users.noreply.github.com>
Date: Fri, 8 Nov 2024 21:40:14 +0000
Subject: [PATCH] deploy: a8b328122d07570dc8bea232dfa30c507e4e8324

---
 API/algs.html        |  11 +-
 API/imfs.html        | 259 +++++++++++++++++++++-
 API/ndblock.html     |  32 ++-
 API/ome_zarr_io.html |   8 +-
 API/seg_process.html | 509 ++++++++++++++++++++++++++++++++++++++++++-
 genindex.html        | 182 ++++++++++++++++
 index.html           |  24 +-
 objects.inv          | Bin 785 -> 1305 bytes
 searchindex.js       |   2 +-
 9 files changed, 1005 insertions(+), 22 deletions(-)

diff --git a/API/algs.html b/API/algs.html
index 650b1d0..5f28ebc 100644
--- a/API/algs.html
+++ b/API/algs.html
@@ -58,7 +58,10 @@
 <li class="toctree-l1"><a class="reference internal" href="imfs.html">cvpl_tools.im.fs.py</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ndblock.html">cvpl_tools.im.ndblock.py</a></li>
 <li class="toctree-l1"><a class="reference internal" href="seg_process.html">cvpl_tools.im.seg_process.py</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">cvpl_tools.im.algs</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">cvpl_tools.im.algs</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.algs.dask_label.label"><code class="docutils literal notranslate"><span class="pre">label()</span></code></a></li>
+</ul>
+</li>
 </ul>
 
         </div>
@@ -89,6 +92,12 @@
 <span id="algs"></span><h1>cvpl_tools/im/algs<a class="headerlink" href="#cvpl-tools-im-algs" title="Permalink to this heading"></a></h1>
 <p>This subdirectory defines relevant algorithms for parallel processing of nd-images.</p>
 <p class="rubric">APIs</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="cvpl_tools.im.algs.dask_label.label">
+<span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.algs.dask_label.</span></span><span class="sig-name descname"><span class="pre">label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dtype</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dtype</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.algs.dask_label.label" title="Permalink to this definition"></a></dt>
+<dd><p>Return (lbl_im, nlbl) where lbl_im is a globally labeled image of the same type/chunk size as the input</p>
+</dd></dl>
+
 </section>
 
 
diff --git a/API/imfs.html b/API/imfs.html
index b27e7be..ee6ad86 100644
--- a/API/imfs.html
+++ b/API/imfs.html
@@ -56,7 +56,32 @@
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="napari_zarr.html">cvpl_tools.ome_zarr.napari.add.py</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ome_zarr_io.html">cvpl_tools.ome_zarr.io.py</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">cvpl_tools.im.fs.py</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">cvpl_tools.im.fs.py</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.fs.save"><code class="docutils literal notranslate"><span class="pre">save()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.fs.load"><code class="docutils literal notranslate"><span class="pre">load()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.fs.display"><code class="docutils literal notranslate"><span class="pre">display()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath"><code class="docutils literal notranslate"><span class="pre">CachePath</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.abs_path"><code class="docutils literal notranslate"><span class="pre">CachePath.abs_path</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.filename"><code class="docutils literal notranslate"><span class="pre">CachePath.filename</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.filename_form_meta"><code class="docutils literal notranslate"><span class="pre">CachePath.filename_form_meta()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.is_dir"><code class="docutils literal notranslate"><span class="pre">CachePath.is_dir</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.meta_from_filename"><code class="docutils literal notranslate"><span class="pre">CachePath.meta_from_filename()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.rel_path"><code class="docutils literal notranslate"><span class="pre">CachePath.rel_path</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath.url"><code class="docutils literal notranslate"><span class="pre">CachePath.url</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory"><code class="docutils literal notranslate"><span class="pre">CacheDirectory</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory.cache"><code class="docutils literal notranslate"><span class="pre">CacheDirectory.cache()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory.cache_im"><code class="docutils literal notranslate"><span class="pre">CacheDirectory.cache_im()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory.cache_subdir"><code class="docutils literal notranslate"><span class="pre">CacheDirectory.cache_subdir()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory.cache_subpath"><code class="docutils literal notranslate"><span class="pre">CacheDirectory.cache_subpath()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory.children_from_path"><code class="docutils literal notranslate"><span class="pre">CacheDirectory.children_from_path()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory.remove_tmp"><code class="docutils literal notranslate"><span class="pre">CacheDirectory.remove_tmp()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.fs.CacheRootDirectory"><code class="docutils literal notranslate"><span class="pre">CacheRootDirectory</span></code></a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="ndblock.html">cvpl_tools.im.ndblock.py</a></li>
 <li class="toctree-l1"><a class="reference internal" href="seg_process.html">cvpl_tools.im.seg_process.py</a></li>
 <li class="toctree-l1"><a class="reference internal" href="algs.html">cvpl_tools.im.algs</a></li>
@@ -90,6 +115,238 @@
 <span id="imfs"></span><h1>cvpl_tools/im/fs.py<a class="headerlink" href="#cvpl-tools-im-fs-py" title="Permalink to this heading"></a></h1>
 <p>View source at <a class="reference external" href="https://github.com/khanlab/cvpl_tools/blob/main/src/cvpl_tools/im/fs.py">fs.py</a>.</p>
 <p class="rubric">APIs</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.save">
+<span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.fs.</span></span><span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">im</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.save" title="Permalink to this definition"></a></dt>
+<dd><p>Save an image object into given path</p>
+<p>Supported im object types:
+- np.ndarray
+- dask.Array
+- cvpl_tools.im.ndblock.NDBlock</p>
+<dl class="simple">
+<dt>Storage options</dt><dd><dl class="simple">
+<dt>preferred_chunksize (tuple[int, …]) = None</dt><dd><p>chunk sizes to save as; will rechunk if different from current size; only applies to dask arrays.</p>
+</dd>
+<dt>multiscale (int) = 0</dt><dd><p>The number of downsample layers for save ome-zarr; only applies if the image is a dask image</p>
+</dd>
+<dt>compressor = None</dt><dd><p>The compressor to use to compress array or chunks</p>
+</dd>
+</dl>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>file</strong> – The full/relative path to the directory to be saved to</p></li>
+<li><p><strong>im</strong> – Object to be saved</p></li>
+<li><p><strong>storage_options</strong> – Specifies options in saving method and saved file format</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.load">
+<span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.fs.</span></span><span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.load" title="Permalink to this definition"></a></dt>
+<dd><p>Load an image from the given directory.</p>
+<p>The image is one saved by cvpl_tools.im.fs.save()</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>file</strong> – Full path to the directory to be read from</p></li>
+<li><p><strong>storage_options</strong> – Specifies options in saving method and saved file format</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Recreated image; this method attempts to keep meta and content of the loaded image stays
+the same as when they are saved</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.display">
+<span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.fs.</span></span><span class="sig-name descname"><span class="pre">display</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.display" title="Permalink to this definition"></a></dt>
+<dd><p>Display an image in the viewer; supports numpy or dask ome zarr image</p>
+<p>The image is one saved by cvpl_tools.im.fs.save()</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>file</strong> – Full path to the directory to be read from</p></li>
+<li><p><strong>viewer_args</strong> – contains viewer and arguments passed to the viewer’s add image functions</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.fs.</span></span><span class="sig-name descname"><span class="pre">CachePath</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#cvpl_tools.im.fs.CacheRootDirectory" title="cvpl_tools.im.fs.CacheRootDirectory"><span class="pre">CacheRootDirectory</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">path_segs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="p"><span class="pre">...</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">meta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory" title="cvpl_tools.im.fs.CacheDirectory"><span class="pre">CacheDirectory</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exists</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">RDirFileSystem</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.CachePath" title="Permalink to this definition"></a></dt>
+<dd><p>A CachePath class is a pointer to a cached location within a hierarchical directory structure.</p>
+<p>CachePath and CacheDirectory are two classes that implements the file-directory programming pattern,
+where CacheDirectory is a subclass of CachePath and contains zero or more CachePath as its children.
+To create a CachePath object, use the CacheDirectory’s cache() function to allocate a new or find
+an existing cache location.</p>
+<p>CachePath as its name suggests is not a folder but only a path. Creating a CachePath object will not
+create the associated file automatically.</p>
+<dl class="py property">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.abs_path">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">abs_path</span></span><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.abs_path" title="Permalink to this definition"></a></dt>
+<dd><p>Obtain the absolute path associated with this CachePath object</p>
+<p>The first time this url is associated with a CachePath object, it’s supposed to be empty and can be used as the
+address to store cache files. Afterward the next time app starts the cache can be read from this url.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.filename">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filename</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.filename" title="Permalink to this definition"></a></dt>
+<dd><p>Returns the filename, the last segment of the path</p>
+<p>This is typically cid prepended with is_dir and is_tmp information; do not call this
+on root directory.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.filename_form_meta">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filename_form_meta</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">meta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.filename_form_meta" title="Permalink to this definition"></a></dt>
+<dd><p>Obtain filename from the meta dict</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>meta</strong> – The dictionary containing meta information for the CachePath object</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A string as the filename of the cached directory or file</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.is_dir">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_dir</span></span><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.is_dir" title="Permalink to this definition"></a></dt>
+<dd><p>Returns True if this is a directory object instead of a file.</p>
+<p>In other words, this function returns False if this is a leaf node.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.meta_from_filename">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">meta_from_filename</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_none_if_malform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.meta_from_filename" title="Permalink to this definition"></a></dt>
+<dd><p>Retrieve meta information from the path</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>file</strong> – filename of the (existing to planning to be created) CachePath object</p></li>
+<li><p><strong>return_none_if_malform</strong> – If True, return None instead of throwing error if a malformed
+filename is given</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dictionary of the meta information</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.rel_path">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">rel_path</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.rel_path" title="Permalink to this definition"></a></dt>
+<dd><p>Obtain the relative os path to the root</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CachePath.url">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">url</span></span><a class="headerlink" href="#cvpl_tools.im.fs.CachePath.url" title="Permalink to this definition"></a></dt>
+<dd><p>Obtain the url associated with this CachePath object</p>
+<p>The first time this url is associated with a CachePath object, it’s supposed to be empty and can be used as the
+address to store cache files. Afterward the next time app starts the cache can be read from this url.</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.fs.</span></span><span class="sig-name descname"><span class="pre">CacheDirectory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">root</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#cvpl_tools.im.fs.CacheRootDirectory" title="cvpl_tools.im.fs.CacheRootDirectory"><span class="pre">CacheRootDirectory</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">path_segs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="p"><span class="pre">...</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_when_done</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">read_if_exists</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory" title="cvpl_tools.im.fs.CacheDirectory"><span class="pre">CacheDirectory</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exists</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory" title="Permalink to this definition"></a></dt>
+<dd><p>A CacheDirectory is a hierarchical directory structure, corresponding to a directory in the os</p>
+<p>CachePath and CacheDirectory are two classes that implements the file-directory programming pattern.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory.cache">
+<span class="sig-name descname"><span class="pre">cache</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory.cache" title="Permalink to this definition"></a></dt>
+<dd><p>Similar to _create_cache(), but use an intermediate object to offset the decision of is_dir</p>
+<p>Often we pass an empty CacheDirectory object to a function, which saves the intermediate results
+in the empty directory. When the function saves a single file, it will prefer to save to a
+CachePath instead of a CacheDirectory. This makes creating CacheDirectory before function call
+inappropriate. To avoid this, we pass in a struct that contains the parent directory and the
+desired path to create either a CachePath or a CacheDirectory, and offset the decision to
+the function itself.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cid</strong> – The cid of either the CachePath or the CacheDirectory</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A CachePointer object of the cache to be created</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory.cache_im">
+<span class="sig-name descname"><span class="pre">cache_im</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fn</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory.cache_im" title="Permalink to this definition"></a></dt>
+<dd><p>Caches an image object</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fn</strong> – Computes the image if it’s not already cached</p></li>
+<li><p><strong>cid</strong> – The cache ID within this directory</p></li>
+<li><p><strong>cache_level</strong> – cache level of this operation; note even if the caching is skipped, if there is
+a cache file already available on disk then the file will still be read</p></li>
+<li><p><strong>viewer_args</strong> – contains viewer and arguments passed to the viewer’s add image functions</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The cached image loaded</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory.cache_subdir">
+<span class="sig-name descname"><span class="pre">cache_subdir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#cvpl_tools.im.fs.CacheDirectory" title="cvpl_tools.im.fs.CacheDirectory"><span class="pre">CacheDirectory</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory.cache_subdir" title="Permalink to this definition"></a></dt>
+<dd><p>Wrapper, calls cache(is_dir=True)</p>
+<p>See the docs for CacheDirectory.cache() for more information.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory.cache_subpath">
+<span class="sig-name descname"><span class="pre">cache_subpath</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#cvpl_tools.im.fs.CachePath" title="cvpl_tools.im.fs.CachePath"><span class="pre">CachePath</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory.cache_subpath" title="Permalink to this definition"></a></dt>
+<dd><p>Wrapper, calls cache(is_dir=False)</p>
+<p>See the docs for CacheDirectory.cache() for more information.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory.children_from_path">
+<span class="sig-name descname"><span class="pre">children_from_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prefix_path_segs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="p"><span class="pre">...</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="#cvpl_tools.im.fs.CachePath" title="cvpl_tools.im.fs.CachePath"><span class="pre">cvpl_tools.im.fs.CachePath</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory.children_from_path" title="Permalink to this definition"></a></dt>
+<dd><p>Examine an existing directory path, return recursively all files and directories as dict.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>prefix_path_segs</strong> – segments prefixing the filenames found under this directory</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Returned json dictionary contains a hierarchical str -&gt; CachePath map; use CachePath.is_dir to
+determine if they contain more children</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheDirectory.remove_tmp">
+<span class="sig-name descname"><span class="pre">remove_tmp</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.CacheDirectory.remove_tmp" title="Permalink to this definition"></a></dt>
+<dd><p>traverse all subnodes and self, removing those with is_tmp=True</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.fs.CacheRootDirectory">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.fs.</span></span><span class="sig-name descname"><span class="pre">CacheRootDirectory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_when_done</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">read_if_exists</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.fs.CacheRootDirectory" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 </section>
 
 
diff --git a/API/ndblock.html b/API/ndblock.html
index 6bff072..79fbe85 100644
--- a/API/ndblock.html
+++ b/API/ndblock.html
@@ -64,6 +64,7 @@
 <li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.is_numpy"><code class="docutils literal notranslate"><span class="pre">NDBlock.is_numpy()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.load"><code class="docutils literal notranslate"><span class="pre">NDBlock.load()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.map_ndblocks"><code class="docutils literal notranslate"><span class="pre">NDBlock.map_ndblocks()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.persist"><code class="docutils literal notranslate"><span class="pre">NDBlock.persist()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.reduce"><code class="docutils literal notranslate"><span class="pre">NDBlock.reduce()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.save"><code class="docutils literal notranslate"><span class="pre">NDBlock.save()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock.select_columns"><code class="docutils literal notranslate"><span class="pre">NDBlock.select_columns()</span></code></a></li>
@@ -120,12 +121,11 @@
 from the side of the tail first</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="cvpl_tools.im.ndblock.NDBlock.as_dask_array">
-<span class="sig-name descname"><span class="pre">as_dask_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tmp_dirpath</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Array</span></span></span><a class="headerlink" href="#cvpl_tools.im.ndblock.NDBlock.as_dask_array" title="Permalink to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">as_dask_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Array</span></span></span><a class="headerlink" href="#cvpl_tools.im.ndblock.NDBlock.as_dask_array" title="Permalink to this definition"></a></dt>
 <dd><p>Get a copy of the array value as dask array</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>tmp_dirpath</strong> – Avoid double computation, best provided if input format
-is ReprFormat.DICT_BLOCK_INDEX_SLICES and is dask instead of numpy</p>
+<dd class="field-odd"><p><strong>storage_options</strong> – Optionally, specify a compression format when persist</p>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p>converted/retrieved dask array</p>
@@ -173,7 +173,8 @@
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>file</strong> – The path to load from, same as used in the save() function</p></li>
-<li><p><strong>storage_options</strong> – Specifies options in saving method and saved file format</p></li>
+<li><p><strong>storage_options</strong> – Specifies options in saving method and saved file format; this includes ‘compressor’ and
+‘port_protocol’</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
@@ -208,6 +209,23 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.ndblock.NDBlock.persist">
+<span class="sig-name descname"><span class="pre">persist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">compressor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.ndblock.NDBlock.persist" title="Permalink to this definition"></a></dt>
+<dd><p>Using dask client persist() to save and reload the NDBlock object</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ndblock</strong> – The NDBlock to be saved</p></li>
+<li><p><strong>compressor</strong> – The compression used</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Reloaded NDBlock object; if is numpy, then no saving is done and the object is directly returned</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="cvpl_tools.im.ndblock.NDBlock.reduce">
 <span class="sig-name descname"><span class="pre">reduce</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">force_numpy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></span><a class="headerlink" href="#cvpl_tools.im.ndblock.NDBlock.reduce" title="Permalink to this definition"></a></dt>
@@ -262,13 +280,11 @@
 
 <dl class="py method">
 <dt class="sig sig-object py" id="cvpl_tools.im.ndblock.NDBlock.to_dask_array">
-<span class="sig-name descname"><span class="pre">to_dask_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tmp_dirpath</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.ndblock.NDBlock.to_dask_array" title="Permalink to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">to_dask_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.ndblock.NDBlock.to_dask_array" title="Permalink to this definition"></a></dt>
 <dd><p>Convert representation format to dask array</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>tmp_dirpath</strong> – An empty path to create a temporary save file, best provided if input format
-is ReprFormat.DICT_BLOCK_INDEX_SLICES and is dask instead of numpy, and you want to
-avoid repeated computations</p>
+<dd class="field-odd"><p><strong>storage_options</strong> – Optionally, specify a compression format when persist</p>
 </dd>
 </dl>
 </dd></dl>
diff --git a/API/ome_zarr_io.html b/API/ome_zarr_io.html
index 4996a53..f29ca9f 100644
--- a/API/ome_zarr_io.html
+++ b/API/ome_zarr_io.html
@@ -157,17 +157,17 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="cvpl_tools.ome_zarr.io.write_ome_zarr_image">
-<span class="sig-prename descclassname"><span class="pre">cvpl_tools.ome_zarr.io.</span></span><span class="sig-name descname"><span class="pre">write_ome_zarr_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ome_zarr_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmp_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">da_arr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lbl_arr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lbl_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_zip</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">MAX_LAYER</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lbl_storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.ome_zarr.io.write_ome_zarr_image" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">cvpl_tools.ome_zarr.io.</span></span><span class="sig-name descname"><span class="pre">write_ome_zarr_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">out_ome_zarr_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmp_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">da_arr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lbl_arr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lbl_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_zip</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">MAX_LAYER</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lbl_storage_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.ome_zarr.io.write_ome_zarr_image" title="Permalink to this definition"></a></dt>
 <dd><p>Write dask array as an ome zarr</p>
 <p>For writing to zip file: due to dask does not directly support write to zip file, we instead create a temp ome zarr
 output and copy it into a zip after done. This is why tmp_path is required if make_zip=True</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ome_zarr_path</strong> – The path to target ome zarr folder, or ome zarr zip folder if make_zip is True</p></li>
+<li><p><strong>out_ome_zarr_path</strong> – The path to target ome zarr folder, or ome zarr zip folder if make_zip is True</p></li>
 <li><p><strong>tmp_path</strong> – temporary files will be stored under this,</p></li>
-<li><p><strong>da_arr</strong> – If provided, this is the array to write at {ome_zarr_path}</p></li>
-<li><p><strong>lbl_arr</strong> – If provided, this is the array to write at {ome_zarr_path}/labels/{lbl_name}</p></li>
+<li><p><strong>da_arr</strong> – If provided, this is the array to write at {out_ome_zarr_path}</p></li>
+<li><p><strong>lbl_arr</strong> – If provided, this is the array to write at {out_ome_zarr_path}/labels/{lbl_name}</p></li>
 <li><p><strong>lbl_name</strong> – name of the folder of the label array</p></li>
 <li><p><strong>make_zip</strong> – bool, if True the output is a zip; if False a folder; if None, then determine based on file suffix</p></li>
 <li><p><strong>MAX_LAYER</strong> – The maximum layer of down sampling; starting at layer=0</p></li>
diff --git a/API/seg_process.html b/API/seg_process.html
index 27ae2f2..3012e8c 100644
--- a/API/seg_process.html
+++ b/API/seg_process.html
@@ -59,11 +59,80 @@
 <li class="toctree-l1"><a class="reference internal" href="imfs.html">cvpl_tools.im.fs.py</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ndblock.html">cvpl_tools.im.ndblock.py</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">cvpl_tools.im.seg_process.py</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#bs-to-os">bs_to_os</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#lc-to-cc">lc_to_cc</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#os-to-cc">os_to_cc</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#os-to-lc">os_to_lc</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#any-to-any">any_to_any</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.SegProcess"><code class="docutils literal notranslate"><span class="pre">SegProcess</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.seg_process.SegProcess.forward"><code class="docutils literal notranslate"><span class="pre">SegProcess.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.BlockToBlockProcess"><code class="docutils literal notranslate"><span class="pre">BlockToBlockProcess</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.seg_process.BlockToBlockProcess.forward"><code class="docutils literal notranslate"><span class="pre">BlockToBlockProcess.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.lc_interpretable_napari"><code class="docutils literal notranslate"><span class="pre">lc_interpretable_napari()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.GaussianBlur"><code class="docutils literal notranslate"><span class="pre">GaussianBlur</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.BSPredictor"><code class="docutils literal notranslate"><span class="pre">BSPredictor</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.SimpleThreshold"><code class="docutils literal notranslate"><span class="pre">SimpleThreshold</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.BlobDog"><code class="docutils literal notranslate"><span class="pre">BlobDog</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.seg_process.BlobDog.forward"><code class="docutils literal notranslate"><span class="pre">BlobDog.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.SumScaledIntensity"><code class="docutils literal notranslate"><span class="pre">SumScaledIntensity</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.seg_process.SumScaledIntensity.forward"><code class="docutils literal notranslate"><span class="pre">SumScaledIntensity.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance"><code class="docutils literal notranslate"><span class="pre">BinaryAndCentroidListToInstance</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.bacl_forward"><code class="docutils literal notranslate"><span class="pre">BinaryAndCentroidListToInstance.bacl_forward()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.forward"><code class="docutils literal notranslate"><span class="pre">BinaryAndCentroidListToInstance.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#bs-to-os">bs_to_os</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.bs_to_os.DirectBSToOS"><code class="docutils literal notranslate"><span class="pre">DirectBSToOS</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.bs_to_os.DirectBSToOS.forward"><code class="docutils literal notranslate"><span class="pre">DirectBSToOS.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.bs_to_os.Watershed3SizesBSToOS"><code class="docutils literal notranslate"><span class="pre">Watershed3SizesBSToOS</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#lc-to-cc">lc_to_cc</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCBySize"><code class="docutils literal notranslate"><span class="pre">CountLCBySize</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCBySize.cc_list"><code class="docutils literal notranslate"><span class="pre">CountLCBySize.cc_list()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCBySize.forward"><code class="docutils literal notranslate"><span class="pre">CountLCBySize.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized"><code class="docutils literal notranslate"><span class="pre">CountLCEdgePenalized</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.cc_list"><code class="docutils literal notranslate"><span class="pre">CountLCEdgePenalized.cc_list()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.forward"><code class="docutils literal notranslate"><span class="pre">CountLCEdgePenalized.forward()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.np_features"><code class="docutils literal notranslate"><span class="pre">CountLCEdgePenalized.np_features()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#os-to-cc">os_to_cc</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.os_to_cc.CountOSBySize"><code class="docutils literal notranslate"><span class="pre">CountOSBySize</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.os_to_cc.CountOSBySize.forward"><code class="docutils literal notranslate"><span class="pre">CountOSBySize.forward()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#os-to-lc">os_to_lc</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.os_to_lc.DirectOSToLC"><code class="docutils literal notranslate"><span class="pre">DirectOSToLC</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.os_to_lc.DirectOSToLC.aggregate_by_id"><code class="docutils literal notranslate"><span class="pre">DirectOSToLC.aggregate_by_id()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.os_to_lc.DirectOSToLC.forward"><code class="docutils literal notranslate"><span class="pre">DirectOSToLC.forward()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#any-to-any">any_to_any</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor"><code class="docutils literal notranslate"><span class="pre">DownsamplingByIntFactor</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor.forward"><code class="docutils literal notranslate"><span class="pre">DownsamplingByIntFactor.forward()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor"><code class="docutils literal notranslate"><span class="pre">UpsamplingByIntFactor</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.forward"><code class="docutils literal notranslate"><span class="pre">UpsamplingByIntFactor.forward()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.np_forward"><code class="docutils literal notranslate"><span class="pre">UpsamplingByIntFactor.np_forward()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="algs.html">cvpl_tools.im.algs</a></li>
@@ -103,12 +172,211 @@
 For general processing whose output are list of centroids, or when input shape of any block is not the same as
 output shape of that block, use <code class="code docutils literal notranslate"><span class="pre">BlockToBlockProcess</span></code>.</p>
 <p class="rubric">APIs</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.SegProcess">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">SegProcess</span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.SegProcess" title="Permalink to this definition"></a></dt>
+<dd><dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.SegProcess.forward">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Any</span></span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.SegProcess.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BlockToBlockProcess">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">BlockToBlockProcess</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">out_dtype</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dtype</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compute_chunk_sizes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.BlockToBlockProcess" title="Permalink to this definition"></a></dt>
+<dd><dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BlockToBlockProcess.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.BlockToBlockProcess.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.lc_interpretable_napari">
+<span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">lc_interpretable_napari</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">layer_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">napari.Viewer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ndim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_features</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">text_color</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'green'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.lc_interpretable_napari" title="Permalink to this definition"></a></dt>
+<dd><p>This function is used to display feature points for LC-typed output</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>layer_name</strong> – displayed name of the layer</p></li>
+<li><p><strong>lc</strong> – The list of features, each row of length (ndim + nextra)</p></li>
+<li><p><strong>viewer</strong> – Napari viewer to add points to</p></li>
+<li><p><strong>ndim</strong> – dimension of the image</p></li>
+<li><p><strong>extra_features</strong> – extra features to be displayed as text</p></li>
+<li><p><strong>text_color</strong> – to be used as display text color</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
 <p class="rubric">Built-in Subclasses for SegProcess</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.GaussianBlur">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">GaussianBlur</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.GaussianBlur" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BSPredictor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">BSPredictor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pred_fn</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Callable</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.BSPredictor" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.SimpleThreshold">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">SimpleThreshold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.SimpleThreshold" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BlobDog">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">BlobDog</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_sigma</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_sigma</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reduce</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.BlobDog" title="Permalink to this definition"></a></dt>
+<dd><dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BlobDog.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float32</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.BlobDog.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.SumScaledIntensity">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">SumScaledIntensity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.008</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_thres</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reduce</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spatial_box_width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.SumScaledIntensity" title="Permalink to this definition"></a></dt>
+<dd><dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.SumScaledIntensity.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.SumScaledIntensity.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.seg_process.</span></span><span class="sig-name descname"><span class="pre">BinaryAndCentroidListToInstance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">maxSplit</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance" title="Permalink to this definition"></a></dt>
+<dd><p>Defines a SegProcess</p>
+<p>This class’ instance forward() takes two inputs: The binary mask segmenting objects, and centroids
+detected by the blobdog algorithm. Then it splits the pixels in the binary mask into instance
+segmentation based on the centroids found by blobdog. The result is a more finely segmented mask
+where objects closer together are more likely to be correctly segmented as two</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.bacl_forward">
+<span class="sig-name descname"><span class="pre">bacl_forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">uint8</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">int32</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.bacl_forward" title="Permalink to this definition"></a></dt>
+<dd><p>For a numpy block and list of centroids in block, return segmentation based on centroids</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">uint8</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">int32</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></span><a class="headerlink" href="#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
 <section id="bs-to-os">
 <h2>bs_to_os<a class="headerlink" href="#bs-to-os" title="Permalink to this heading"></a></h2>
 <p>binary segmentation to ordinal segmentation</p>
 <p>This section contains algorithms whose input is binary (0-1) segmentation mask, and output is instance segmentation
 (0-N) integer mask where the output ndarray is of the same shape as input.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.bs_to_os.DirectBSToOS">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.bs_to_os.</span></span><span class="sig-name descname"><span class="pre">DirectBSToOS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">is_global</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.bs_to_os.DirectBSToOS" title="Permalink to this definition"></a></dt>
+<dd><dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.bs_to_os.DirectBSToOS.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a></span></span><a class="headerlink" href="#cvpl_tools.im.process.bs_to_os.DirectBSToOS.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.bs_to_os.Watershed3SizesBSToOS">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.bs_to_os.</span></span><span class="sig-name descname"><span class="pre">Watershed3SizesBSToOS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">size_thres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">60.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist_thres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rst</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size_thres2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist_thres2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rst2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">60.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.bs_to_os.Watershed3SizesBSToOS" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 </section>
 <section id="lc-to-cc">
 <h2>lc_to_cc<a class="headerlink" href="#lc-to-cc" title="Permalink to this heading"></a></h2>
@@ -116,24 +384,255 @@ <h2>lc_to_cc<a class="headerlink" href="#lc-to-cc" title="Permalink to this head
 <p>This section contains algorithms whose input is a 2d array or a 2d array of each block describing the centroid
 locations and meta information about the objects associated with the centroids in each block. The output is a single
 number summarizing statistics for each block.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCBySize">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.lc_to_cc.</span></span><span class="sig-name descname"><span class="pre">CountLCBySize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">size_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">25.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volume_weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.006</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">border_params</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(3.0,</span> <span class="pre">-0.5,</span> <span class="pre">2.0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reduce</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCBySize" title="Permalink to this definition"></a></dt>
+<dd><p>Counting list of cells by size</p>
+<p>Several features:
+1. A size threshold, below which each contour is counted as a single cell (or part of a single cell,
+in the case it is neighbor to boundary of the image)
+2. Above size threshold, the contour is seen as a cluster of cells an estimate of cell count is given
+based on the volume of the contour
+3. For cells on the boundary location, their estimated ncell is penalized according to the distance
+between the cell centroid and the boundary of the image; if the voxels of the cell do not touch
+edge, this penalty does not apply
+4. A min_size threshold, below (&lt;=) which the contour is simply discarded because it’s likely just
+an artifact</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCBySize.cc_list">
+<span class="sig-name descname"><span class="pre">cc_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ndim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">os_shape</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCBySize.cc_list" title="Permalink to this definition"></a></dt>
+<dd><p>Assumption: lc[:, ndim] is nvoxel and lc[:, ndim + 1] is edge_contact</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCBySize.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ndim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCBySize.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.lc_to_cc.</span></span><span class="sig-name descname"><span class="pre">CountLCEdgePenalized</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chunks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">border_params</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(3.0,</span> <span class="pre">-0.5,</span> <span class="pre">2.0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reduce</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized" title="Permalink to this definition"></a></dt>
+<dd><p>From a list of cell centroid locations, calculate a cell count estimate</p>
+<p>You need to provide an image_shape parameter due to the fact that lc does not contain
+information about input image shape</p>
+<p>Each centroid is simply treated as 1 cell when they are sufficiently far from the edge,
+but as they get closer to the edge the divisor becomes &gt;1. and their estimate decreases
+towards 0, since cells near the edge may be double-counted (or triple or more counted
+if at a corner etc.)</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.cc_list">
+<span class="sig-name descname"><span class="pre">cc_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.cc_list" title="Permalink to this definition"></a></dt>
+<dd><p>Returns a cell count estimate for each contour in the list of centroids</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>lc</strong> – The list of centroids to be given cell estimates for</p></li>
+<li><p><strong>block_index</strong> – The index of the block which this lc corresponds to</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A 1-d list, each element is a scalar cell count for the corresponding contour centroid in lc</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.np_features">
+<span class="sig-name descname"><span class="pre">np_features</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.np_features" title="Permalink to this definition"></a></dt>
+<dd><p>Calculate cell counts, then concat centroid locations to the left of cell counts</p>
+</dd></dl>
+
+</dd></dl>
+
 </section>
 <section id="os-to-cc">
 <h2>os_to_cc<a class="headerlink" href="#os-to-cc" title="Permalink to this heading"></a></h2>
 <p>oridnal segmentation to cell counts</p>
 <p>This section contains algorithms whose input is instance segmentation (0-N) integer mask where the output is a single
 number summarizing statistics for each block.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.os_to_cc.CountOSBySize">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.os_to_cc.</span></span><span class="sig-name descname"><span class="pre">CountOSBySize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">size_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">25.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volume_weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.006</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">border_params</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(3.0,</span> <span class="pre">-0.5,</span> <span class="pre">2.0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reduce</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_global</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.os_to_cc.CountOSBySize" title="Permalink to this definition"></a></dt>
+<dd><p>Counting ordinal segmentation contours</p>
+<p>Several features:
+1. A size threshold, below which each contour is counted as a single cell (or part of a single cell,
+in the case it is neighbor to boundary of the image)
+2. Above size threshold, the contour is seen as a cluster of cells an estimate of cell count is given
+based on the volume of the contour
+3. For cells on the boundary location, their estimated ncell is penalized according to the distance
+between the cell centroid and the boundary of the image; if the voxels of the cell do not touch
+edge, this penalty does not apply
+4. A min_size threshold, below (&lt;=) which the contour is simply discarded because it’s likely just
+an artifact</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.os_to_cc.CountOSBySize.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">int32</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.os_to_cc.CountOSBySize.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
 </section>
 <section id="os-to-lc">
 <h2>os_to_lc<a class="headerlink" href="#os-to-lc" title="Permalink to this heading"></a></h2>
 <p>ordinal segmentation to list of centroids</p>
 <p>This section contains algorithms whose input is instance segmentation (0-N) integer mask where the output is a list
 of centroids with meta information.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.os_to_lc.DirectOSToLC">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.os_to_lc.</span></span><span class="sig-name descname"><span class="pre">DirectOSToLC</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reduce</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_global</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ex_statistics</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.os_to_lc.DirectOSToLC" title="Permalink to this definition"></a></dt>
+<dd><p>Convert a 0-N contour mask to a list of N centroids, one for each contour</p>
+<p>The converted list of centroids is in the same order as the original contour order (The contour labeled
+1 will come first and before contour labeled 2, 3 and so on)</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.os_to_lc.DirectOSToLC.aggregate_by_id">
+<span class="sig-name descname"><span class="pre">aggregate_by_id</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.os_to_lc.DirectOSToLC.aggregate_by_id" title="Permalink to this definition"></a></dt>
+<dd><p>Aggregate self._ndblock by id</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.os_to_lc.DirectOSToLC.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">int32</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="ndblock.html#cvpl_tools.im.ndblock.NDBlock" title="cvpl_tools.im.ndblock.NDBlock"><span class="pre">NDBlock</span></a><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.os_to_lc.DirectOSToLC.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Compute outputs from inputs (args)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – args inputs to forward()</p></li>
+<li><p><strong>viewer_args</strong> – If not specified, this is just a forward step; if specified, visualization of the step
+underlying working mechanism will be displayed in Napari viewer object viewer_args[‘viewer’] for
+interpretation of results and debugging purposes</p></li>
+<li><p><strong>**kwargs</strong> – kwargs inputs to forward</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>computed output</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
 </section>
 <section id="any-to-any">
 <h2>any_to_any<a class="headerlink" href="#any-to-any" title="Permalink to this heading"></a></h2>
 <p>other</p>
 <p>This sections contain image processing steps whose inputs and outputs may adapt to different types of data or are not
 adequately described by the current classifications.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.any_to_any.</span></span><span class="sig-name descname"><span class="pre">DownsamplingByIntFactor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor" title="Permalink to this definition"></a></dt>
+<dd><p><em>DEPRECATED</em></p>
+<p>use cvpl_tools.im.algs.dask_ndinterp.scale_nearest instead</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></span><a class="headerlink" href="#cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Downsample the image and</p>
+<p>The function will display the downsampled image if viewer is provided in viewer_args, so make sure
+you set is_label to True if the image is a label instead of brightness/RGB</p>
+<p>If you want displayed image to be of the same scale of original, set the scale in viewer_args
+correspondingly</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>im</strong> – Image to be downsampled (np or dask array)</p></li>
+<li><p><strong>cid</strong> – Caching id under the current tmp directory</p></li>
+<li><p><strong>viewer_args</strong> – Arguments for the viewer</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The down-sampled image</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cvpl_tools.im.process.any_to_any.</span></span><span class="sig-name descname"><span class="pre">UpsamplingByIntFactor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor" title="Permalink to this definition"></a></dt>
+<dd><p><em>DEPRECATED</em></p>
+<p>use cvpl_tools.im.algs.dask_ndinterp.scale_nearest instead</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.forward">
+<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cptr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CachePointer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewer_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Array</span></span></span><a class="headerlink" href="#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.forward" title="Permalink to this definition"></a></dt>
+<dd><p>Upsample the image</p>
+<p>The function will display the upsampled image if viewer is provided in viewer_args, so make sure
+you set is_label to True if the image is a label instead of brightness/RGB</p>
+<p>If you want displayed image to be of the same scale of original, set the scale in viewer_args
+correspondingly</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>im</strong> – Image to be upsampled (np or dask array)</p></li>
+<li><p><strong>cid</strong> – Caching id under the current tmp directory</p></li>
+<li><p><strong>viewer_args</strong> – Arguments for the viewer</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The up-sampled image</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.np_forward">
+<span class="sig-name descname"><span class="pre">np_forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">im</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">_ScalarType_co</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.np_forward" title="Permalink to this definition"></a></dt>
+<dd><p>Calculate cell counts, then concat centroid locations to the left of cell counts</p>
+</dd></dl>
+
+</dd></dl>
+
 </section>
 </section>
 
diff --git a/genindex.html b/genindex.html
index dcb25ee..1687795 100644
--- a/genindex.html
+++ b/genindex.html
@@ -87,27 +87,149 @@ <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
  <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#F"><strong>F</strong></a>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#I"><strong>I</strong></a>
  | <a href="#L"><strong>L</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#N"><strong>N</strong></a>
+ | <a href="#P"><strong>P</strong></a>
  | <a href="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
  | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
  | <a href="#W"><strong>W</strong></a>
  
 </div>
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.abs_path">abs_path (cvpl_tools.im.fs.CachePath property)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.os_to_lc.DirectOSToLC.aggregate_by_id">aggregate_by_id() (cvpl_tools.im.process.os_to_lc.DirectOSToLC method)</a>
+</li>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.as_dask_array">as_dask_array() (cvpl_tools.im.ndblock.NDBlock method)</a>
 </li>
   </ul></td>
 </tr></table>
 
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.bacl_forward">bacl_forward() (cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance method)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance">BinaryAndCentroidListToInstance (class in cvpl_tools.im.seg_process)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BlobDog">BlobDog (class in cvpl_tools.im.seg_process)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BlockToBlockProcess">BlockToBlockProcess (class in cvpl_tools.im.seg_process)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BSPredictor">BSPredictor (class in cvpl_tools.im.seg_process)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory.cache">cache() (cvpl_tools.im.fs.CacheDirectory method)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory.cache_im">cache_im() (cvpl_tools.im.fs.CacheDirectory method)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory.cache_subdir">cache_subdir() (cvpl_tools.im.fs.CacheDirectory method)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory.cache_subpath">cache_subpath() (cvpl_tools.im.fs.CacheDirectory method)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory">CacheDirectory (class in cvpl_tools.im.fs)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath">CachePath (class in cvpl_tools.im.fs)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheRootDirectory">CacheRootDirectory (class in cvpl_tools.im.fs)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCBySize.cc_list">cc_list() (cvpl_tools.im.process.lc_to_cc.CountLCBySize method)</a>
+
+      <ul>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.cc_list">(cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized method)</a>
+</li>
+      </ul></li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory.children_from_path">children_from_path() (cvpl_tools.im.fs.CacheDirectory method)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCBySize">CountLCBySize (class in cvpl_tools.im.process.lc_to_cc)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized">CountLCEdgePenalized (class in cvpl_tools.im.process.lc_to_cc)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.os_to_cc.CountOSBySize">CountOSBySize (class in cvpl_tools.im.process.os_to_cc)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.bs_to_os.DirectBSToOS">DirectBSToOS (class in cvpl_tools.im.process.bs_to_os)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.os_to_lc.DirectOSToLC">DirectOSToLC (class in cvpl_tools.im.process.os_to_lc)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.display">display() (in module cvpl_tools.im.fs)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor">DownsamplingByIntFactor (class in cvpl_tools.im.process.any_to_any)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.filename">filename (cvpl_tools.im.fs.CachePath property)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.filename_form_meta">filename_form_meta() (cvpl_tools.im.fs.CachePath static method)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor.forward">forward() (cvpl_tools.im.process.any_to_any.DownsamplingByIntFactor method)</a>
+
+      <ul>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.forward">(cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.bs_to_os.DirectBSToOS.forward">(cvpl_tools.im.process.bs_to_os.DirectBSToOS method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCBySize.forward">(cvpl_tools.im.process.lc_to_cc.CountLCBySize method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.forward">(cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.os_to_cc.CountOSBySize.forward">(cvpl_tools.im.process.os_to_cc.CountOSBySize method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.process.os_to_lc.DirectOSToLC.forward">(cvpl_tools.im.process.os_to_lc.DirectOSToLC method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance.forward">(cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BlobDog.forward">(cvpl_tools.im.seg_process.BlobDog method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.BlockToBlockProcess.forward">(cvpl_tools.im.seg_process.BlockToBlockProcess method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.SegProcess.forward">(cvpl_tools.im.seg_process.SegProcess method)</a>
+</li>
+        <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.SumScaledIntensity.forward">(cvpl_tools.im.seg_process.SumScaledIntensity method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.GaussianBlur">GaussianBlur (class in cvpl_tools.im.seg_process)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.get_chunksize">get_chunksize() (cvpl_tools.im.ndblock.NDBlock method)</a>
 </li>
@@ -116,6 +238,10 @@ <h2 id="G">G</h2>
 
 <h2 id="I">I</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.is_dir">is_dir (cvpl_tools.im.fs.CachePath property)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.is_numpy">is_numpy() (cvpl_tools.im.ndblock.NDBlock method)</a>
 </li>
@@ -125,8 +251,16 @@ <h2 id="I">I</h2>
 <h2 id="L">L</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/algs.html#cvpl_tools.im.algs.dask_label.label">label() (in module cvpl_tools.im.algs.dask_label)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.lc_interpretable_napari">lc_interpretable_napari() (in module cvpl_tools.im.seg_process)</a>
+</li>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.load">load() (cvpl_tools.im.ndblock.NDBlock static method)</a>
+
+      <ul>
+        <li><a href="API/imfs.html#cvpl_tools.im.fs.load">(in module cvpl_tools.im.fs)</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ome_zarr_io.html#cvpl_tools.ome_zarr.io.load_dask_array_from_path">load_dask_array_from_path() (in module cvpl_tools.ome_zarr.io)</a>
@@ -140,6 +274,10 @@ <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.map_ndblocks">map_ndblocks() (cvpl_tools.im.ndblock.NDBlock static method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.meta_from_filename">meta_from_filename() (cvpl_tools.im.fs.CachePath static method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -148,6 +286,20 @@ <h2 id="N">N</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock">NDBlock (class in cvpl_tools.im.ndblock)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized.np_features">np_features() (cvpl_tools.im.process.lc_to_cc.CountLCEdgePenalized method)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor.np_forward">np_forward() (cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.persist">persist() (cvpl_tools.im.ndblock.NDBlock method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -156,9 +308,13 @@ <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.reduce">reduce() (cvpl_tools.im.ndblock.NDBlock method)</a>
+</li>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.rel_path">rel_path (cvpl_tools.im.fs.CachePath property)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory.remove_tmp">remove_tmp() (cvpl_tools.im.fs.CacheDirectory method)</a>
+</li>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.ReprFormat">ReprFormat (class in cvpl_tools.im.ndblock)</a>
 </li>
   </ul></td>
@@ -168,12 +324,22 @@ <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.save">save() (cvpl_tools.im.ndblock.NDBlock static method)</a>
+
+      <ul>
+        <li><a href="API/imfs.html#cvpl_tools.im.fs.save">(in module cvpl_tools.im.fs)</a>
+</li>
+      </ul></li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.SegProcess">SegProcess (class in cvpl_tools.im.seg_process)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.select_columns">select_columns() (cvpl_tools.im.ndblock.NDBlock method)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.SimpleThreshold">SimpleThreshold (class in cvpl_tools.im.seg_process)</a>
 </li>
       <li><a href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock.sum">sum() (cvpl_tools.im.ndblock.NDBlock method)</a>
+</li>
+      <li><a href="API/seg_process.html#cvpl_tools.im.seg_process.SumScaledIntensity">SumScaledIntensity (class in cvpl_tools.im.seg_process)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -192,8 +358,24 @@ <h2 id="T">T</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.any_to_any.UpsamplingByIntFactor">UpsamplingByIntFactor (class in cvpl_tools.im.process.any_to_any)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/imfs.html#cvpl_tools.im.fs.CachePath.url">url (cvpl_tools.im.fs.CachePath property)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="W">W</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="API/seg_process.html#cvpl_tools.im.process.bs_to_os.Watershed3SizesBSToOS">Watershed3SizesBSToOS (class in cvpl_tools.im.process.bs_to_os)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/ome_zarr_io.html#cvpl_tools.ome_zarr.io.write_ome_zarr_image">write_ome_zarr_image() (in module cvpl_tools.ome_zarr.io)</a>
 </li>
diff --git a/index.html b/index.html
index cf69ee5..d6b5f75 100644
--- a/index.html
+++ b/index.html
@@ -148,13 +148,30 @@ <h1>Introduction - cvpl_tools documentation<a class="headerlink" href="#introduc
 <li class="toctree-l2"><a class="reference internal" href="API/ome_zarr_io.html#cvpl_tools.ome_zarr.io.write_ome_zarr_image"><code class="docutils literal notranslate"><span class="pre">write_ome_zarr_image()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="API/imfs.html">cvpl_tools.im.fs.py</a></li>
+<li class="toctree-l1"><a class="reference internal" href="API/imfs.html">cvpl_tools.im.fs.py</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="API/imfs.html#cvpl_tools.im.fs.save"><code class="docutils literal notranslate"><span class="pre">save()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/imfs.html#cvpl_tools.im.fs.load"><code class="docutils literal notranslate"><span class="pre">load()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/imfs.html#cvpl_tools.im.fs.display"><code class="docutils literal notranslate"><span class="pre">display()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/imfs.html#cvpl_tools.im.fs.CachePath"><code class="docutils literal notranslate"><span class="pre">CachePath</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/imfs.html#cvpl_tools.im.fs.CacheDirectory"><code class="docutils literal notranslate"><span class="pre">CacheDirectory</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/imfs.html#cvpl_tools.im.fs.CacheRootDirectory"><code class="docutils literal notranslate"><span class="pre">CacheRootDirectory</span></code></a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="API/ndblock.html">cvpl_tools.im.ndblock.py</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="API/ndblock.html#cvpl_tools.im.ndblock.NDBlock"><code class="docutils literal notranslate"><span class="pre">NDBlock</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="API/ndblock.html#cvpl_tools.im.ndblock.ReprFormat"><code class="docutils literal notranslate"><span class="pre">ReprFormat</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="API/seg_process.html">cvpl_tools.im.seg_process.py</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.SegProcess"><code class="docutils literal notranslate"><span class="pre">SegProcess</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.BlockToBlockProcess"><code class="docutils literal notranslate"><span class="pre">BlockToBlockProcess</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.lc_interpretable_napari"><code class="docutils literal notranslate"><span class="pre">lc_interpretable_napari()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.GaussianBlur"><code class="docutils literal notranslate"><span class="pre">GaussianBlur</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.BSPredictor"><code class="docutils literal notranslate"><span class="pre">BSPredictor</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.SimpleThreshold"><code class="docutils literal notranslate"><span class="pre">SimpleThreshold</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.BlobDog"><code class="docutils literal notranslate"><span class="pre">BlobDog</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.SumScaledIntensity"><code class="docutils literal notranslate"><span class="pre">SumScaledIntensity</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#cvpl_tools.im.seg_process.BinaryAndCentroidListToInstance"><code class="docutils literal notranslate"><span class="pre">BinaryAndCentroidListToInstance</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#bs-to-os">bs_to_os</a></li>
 <li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#lc-to-cc">lc_to_cc</a></li>
 <li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#os-to-cc">os_to_cc</a></li>
@@ -162,7 +179,10 @@ <h1>Introduction - cvpl_tools documentation<a class="headerlink" href="#introduc
 <li class="toctree-l2"><a class="reference internal" href="API/seg_process.html#any-to-any">any_to_any</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="API/algs.html">cvpl_tools.im.algs</a></li>
+<li class="toctree-l1"><a class="reference internal" href="API/algs.html">cvpl_tools.im.algs</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="API/algs.html#cvpl_tools.im.algs.dask_label.label"><code class="docutils literal notranslate"><span class="pre">label()</span></code></a></li>
+</ul>
+</li>
 </ul>
 </div>
 </section>
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diff --git a/searchindex.js b/searchindex.js
index a2accb9..0141ff3 100644
--- a/searchindex.js
+++ b/searchindex.js
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