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phasorpy · Jun 24, 2024 · 88edf18 · 88edf18
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diff --git a/main/_downloads/315c4c52fb68082a731b192d944e2ede/tutorials_python.zip b/main/_downloads/315c4c52fb68082a731b192d944e2ede/tutorials_python.zip
diff --git a/main/_downloads/a5659940aa3f8f568547d47752a43172/tutorials_jupyter.zip b/main/_downloads/a5659940aa3f8f568547d47752a43172/tutorials_jupyter.zip
diff --git a/main/_images/sphx_glr_phasorpy_components_002.png b/main/_images/sphx_glr_phasorpy_components_002.png
diff --git a/main/_images/sphx_glr_phasorpy_components_003.png b/main/_images/sphx_glr_phasorpy_components_003.png
diff --git a/main/_images/sphx_glr_phasorpy_components_thumb.png b/main/_images/sphx_glr_phasorpy_components_thumb.png
diff --git a/main/_images/sphx_glr_phasorpy_phasor_from_lifetime_005.png b/main/_images/sphx_glr_phasorpy_phasor_from_lifetime_005.png
diff --git a/main/_images/sphx_glr_phasorpy_phasorplot_007.png b/main/_images/sphx_glr_phasorpy_phasorplot_007.png
diff --git a/main/_images/sphx_glr_phasorpy_phasorplot_008.png b/main/_images/sphx_glr_phasorpy_phasorplot_008.png
diff --git a/main/_images/sphx_glr_phasorpy_phasorplot_010.png b/main/_images/sphx_glr_phasorpy_phasorplot_010.png
diff --git a/main/_images/sphx_glr_phasorpy_phasorplot_012.png b/main/_images/sphx_glr_phasorpy_phasorplot_012.png
diff --git a/main/_images/sphx_glr_phasorpy_phasorplot_013.png b/main/_images/sphx_glr_phasorpy_phasorplot_013.png
diff --git a/main/_images/sphx_glr_phasorpy_phasorplot_thumb.png b/main/_images/sphx_glr_phasorpy_phasorplot_thumb.png
diff --git a/main/_sources/phasor_approach.rst.txt b/main/_sources/phasor_approach.rst.txt
@@ -180,34 +180,22 @@ approach to analyze fluorescence time-resolved or spectral images:
   is a napari plugin for real-time TCSPC-FLIM analysis based on FLIMLib.
   The plugin is distributed under the GPLv3 license.
 
--
-  .. _hysp:
-
-  `HySP <https://bioimage.usc.edu/software.html#HySP>`_
+- `HySP <https://bioimage.usc.edu/software.html#HySP>`_
   is a free, closed-source, multi-platform desktop application developed by
   Francesco Cutrale for the analysis of multi-dimensional, hyper- and
   multi-spectral data using the phasor approach.
 
--
-  .. _flute:
-
-  `FLUTE <https://github.com/LaboratoryOpticsBiosciences/FLUTE>`_,
+- `FLUTE <https://github.com/LaboratoryOpticsBiosciences/FLUTE>`_,
   the Fluorescence Lifetime Ultimate Explorer, is an open-source Python GUI
   for interactive phasor analysis of FLIM data developed by Chiara Stringari
   and others. The software is distributed under the GPL license.
 
--
-  .. _flim_tools:
-
-  `FLIM_tools <https://github.com/jayunruh/FLIM_tools>`_
+- `FLIM_tools <https://github.com/jayunruh/FLIM_tools>`_
   is an open-source Python library for linear unmixing and phasor tools for
   FLIM analysis developed by Jay Unruh. The library is distributed under
   the GPL2 license.
 
--
-  .. _tttrlib:
-
-  `tttrlib <https://github.com/Fluorescence-Tools/tttrlib>`_
+- `tttrlib <https://github.com/Fluorescence-Tools/tttrlib>`_
   is an open-source C++ and Python library to read, write, and process
   time-tagged time-resolved (TTTR) data. It includes functions for computing
   and correcting phasor coordinates. The library is distributed under the
@@ -221,29 +209,20 @@ approach to analyze fluorescence time-resolved or spectral images:
   segmentation, pH correlation, nanoscale effects, and precise quantification.
   The notebook is distributed under CC BY-NC 4.0.
 
--
-  .. _flimlib:
-
-  `FLIMLib <https://flimlib.github.io>`_ is an exponential curve fitting
+- `FLIMLib <https://flimlib.github.io>`_ is an exponential curve fitting
   library used for Fluorescent Lifetime Imaging (FLIM). It includes a function
   to calculate phasor coordinates from time-resolved signals.
   FLIMLib is licensed under the GPL v3.
 
--
-  .. _flimfit:
-
-  `FLIMfit <https://flimfit.org/>`_  is an open-source, MATLAB-based tool
+- `FLIMfit <https://flimfit.org/>`_  is an open-source, MATLAB-based tool
   to analyse and visualize time-resolved data from FLIM measurements
   including TCSPC and wide-field time-gated imaging.
   It includes a segmentation tool based on the phasor approach.
   The affiliated `FlimReader <https://github.com/flimfit/FlimReader>`_ library
   provides file readers for FLIM data including TTTR.
   FLIMfit is licensed under the GPL v2.
 
--
-  .. _pam:
-
-  `PAM <https://pam.readthedocs.io/en/latest/phasor.html>`_
+- `PAM <https://pam.readthedocs.io/en/latest/phasor.html>`_
   is an open-source GUI-based MATLAB package for the analysis of fluorescence
   experiments. The phasor analysis includes region of interests, fractions,
   triangular mixtures, and FRET estimation. PAM is licensed under the GPL v3.
@@ -266,19 +245,13 @@ approach to analyze fluorescence time-resolved or spectral images:
   techniques, and an application programming interface. Python modules
   by FLIM LABS are available on `GitHub <https://github.com/FLIMLABS>`_.
 
--
-  .. _vistavision:
-
-  `VistaVision <https://iss.com/software/vistavision>`_
+- `VistaVision <https://iss.com/software/vistavision>`_
   is a commercial Windows desktop software by ISS, Inc., for confocal
   microscopy applications, including instrument control, data acquisition,
   and data processing. It performs image segmentation of FLIM images via
   the phasor plot.
 
--
-  .. _spcimage:
-
-  `SPCImage <https://www.becker-hickl.com/literature/documents/flim/spcimage-ng/>`_
+- `SPCImage <https://www.becker-hickl.com/literature/documents/flim/spcimage-ng/>`_
   is a commercial Windows desktop software by Becker & Hickl (tm) for
   TCSPC-FLIM data analysis. It performs image segmentation of time-resolved
   data via the phasor plot.
@@ -291,19 +264,18 @@ approach to analyze fluorescence time-resolved or spectral images:
   The software allows, by using phasors, to follow microenvironmental changes,
   select components to multiplex signal, and determine FRET efficiency.
 
--
-  .. _luminosa:
-
-  `Luminosa <https://www.picoquant.com/products/category/fluorescence-microscopes/luminosa-single-photon-counting-confocal-microscope#documents>`_
+- `Luminosa <https://www.picoquant.com/products/category/fluorescence-microscopes/luminosa-single-photon-counting-confocal-microscope#documents>`_
   is a commercial Windows desktop software by PicoQuant GmbH, which includes
   single molecule detection, FCS, and time-resolved imaging methods.
   The InstaFLIM module allows simultaneous TCSPC and phasor analysis
   options for ROI determination.
 
--
-  .. _flimfast:
+- `EzTime <https://www.horiba.com/int/scientific/products/detail/action/show/Product/eztime-software-6283/>`_
+  is a commercial software by HORIBA Scientific. It allows real-time TCSPC
+  image analysis and visualization, including phasor plots, in conjunction
+  with the FLIMera wide-field camera.
 
-  `FlimFast <https://www.cgohlke.com/flimfast/>`_
+- `FlimFast <https://www.cgohlke.com/flimfast/>`_
   was a research-grade Windows desktop software for frequency-domain,
   full-field, fluorescence lifetime imaging at video rate, developed by
   Christoph Gohlke during 2000-2002 at UIUC. It enabled phasor vs intensity

diff --git a/main/_sources/sg_execution_times.rst.txt b/main/_sources/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:20.993** total execution time for 7 files **from all galleries**:
+**00:24.088** total execution time for 7 files **from all galleries**:
 
 .. container::
 
@@ -32,24 +32,24 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``../tutorials/benchmarks/phasorpy_phasor_from_signal.py``)
-     - 00:09.567
-     - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_introduction.py` (``../tutorials/phasorpy_introduction.py``)
-     - 00:08.227
+     - 00:11.222
+     - 0.0
+   * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``../tutorials/benchmarks/phasorpy_phasor_from_signal.py``)
+     - 00:09.665
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_fret.py` (``../tutorials/phasorpy_fret.py``)
-     - 00:01.684
+     - 00:01.687
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasorplot.py` (``../tutorials/phasorpy_phasorplot.py``)
      - 00:00.669
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasor_from_lifetime.py` (``../tutorials/phasorpy_phasor_from_lifetime.py``)
-     - 00:00.447
+     - 00:00.445
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_components.py` (``../tutorials/phasorpy_components.py``)
-     - 00:00.350
+     - 00:00.351
      - 0.0
    * - :ref:`sphx_glr_tutorials_misc_phasorpy_logo.py` (``../tutorials/misc/phasorpy_logo.py``)
-     - 00:00.048
+     - 00:00.049
      - 0.0
diff --git a/main/_sources/tutorials/benchmarks/phasorpy_phasor_from_signal.rst.txt b/main/_sources/tutorials/benchmarks/phasorpy_phasor_from_signal.rst.txt
@@ -147,36 +147,36 @@ and number of threads:
 
     harmonics 1
       axis -1
-        phasor_from_signal       0.054s   1.00
-          threads 2              0.032s   0.58
-        phasor_from_signal_fft   0.396s   7.33
-          scipy_fft              0.391s   7.25
+        phasor_from_signal       0.055s   1.00
+          threads 2              0.031s   0.58
+        phasor_from_signal_fft   0.401s   7.33
+          scipy_fft              0.397s   7.26
       axis 0
-        phasor_from_signal       0.163s   3.03
-          threads 2              0.080s   1.49
-        phasor_from_signal_fft   0.682s  12.64
-          scipy_fft              0.474s   8.79
+        phasor_from_signal       0.164s   3.00
+          threads 2              0.080s   1.47
+        phasor_from_signal_fft   0.685s  12.54
+          scipy_fft              0.478s   8.75
       axis 2
-        phasor_from_signal       0.054s   1.01
-          threads 2              0.031s   0.58
-        phasor_from_signal_fft   0.393s   7.29
-          scipy_fft              0.389s   7.22
+        phasor_from_signal       0.054s   0.99
+          threads 2              0.032s   0.58
+        phasor_from_signal_fft   0.402s   7.35
+          scipy_fft              0.398s   7.28
     harmonics 8
       axis -1
-        phasor_from_signal       0.436s   8.09
-          threads 2              0.244s   4.53
-        phasor_from_signal_fft   0.410s   7.61
-          scipy_fft              0.401s   7.44
+        phasor_from_signal       0.440s   8.05
+          threads 2              0.249s   4.56
+        phasor_from_signal_fft   0.416s   7.62
+          scipy_fft              0.414s   7.58
       axis 0
-        phasor_from_signal       1.303s  24.16
-          threads 2              0.660s  12.23
-        phasor_from_signal_fft   0.683s  12.66
-          scipy_fft              0.477s   8.84
+        phasor_from_signal       1.308s  23.96
+          threads 2              0.659s  12.07
+        phasor_from_signal_fft   0.691s  12.66
+          scipy_fft              0.481s   8.80
       axis 2
-        phasor_from_signal       0.434s   8.04
-          threads 2              0.248s   4.60
-        phasor_from_signal_fft   0.408s   7.57
-          scipy_fft              0.402s   7.45
+        phasor_from_signal       0.433s   7.92
+          threads 2              0.247s   4.52
+        phasor_from_signal_fft   0.416s   7.62
+          scipy_fft              0.411s   7.52
 
 
 
@@ -255,7 +255,7 @@ when computing large number of harmonics with an optimized FFT function.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 9.567 seconds)
+   **Total running time of the script:** (0 minutes 9.665 seconds)
 
 
 .. _sphx_glr_download_tutorials_benchmarks_phasorpy_phasor_from_signal.py:

diff --git a/main/_sources/tutorials/benchmarks/sg_execution_times.rst.txt b/main/_sources/tutorials/benchmarks/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:09.567** total execution time for 1 file **from tutorials/benchmarks**:
+**00:09.665** total execution time for 1 file **from tutorials/benchmarks**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``phasorpy_phasor_from_signal.py``)
-     - 00:09.567
+     - 00:09.665
      - 0.0
diff --git a/main/_sources/tutorials/misc/phasorpy_logo.rst.txt b/main/_sources/tutorials/misc/phasorpy_logo.rst.txt
@@ -60,7 +60,7 @@ Create the PhasorPy logo using the PhasorPy library.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.048 seconds)
+   **Total running time of the script:** (0 minutes 0.049 seconds)
 
 
 .. _sphx_glr_download_tutorials_misc_phasorpy_logo.py:

diff --git a/main/_sources/tutorials/misc/sg_execution_times.rst.txt b/main/_sources/tutorials/misc/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.048** total execution time for 1 file **from tutorials/misc**:
+**00:00.049** total execution time for 1 file **from tutorials/misc**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_misc_phasorpy_logo.py` (``phasorpy_logo.py``)
-     - 00:00.048
+     - 00:00.049
      - 0.0
diff --git a/main/_sources/tutorials/phasorpy_components.rst.txt b/main/_sources/tutorials/phasorpy_components.rst.txt
@@ -211,7 +211,7 @@ sphinx_gallery_thumbnail_number = 2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.350 seconds)
+   **Total running time of the script:** (0 minutes 0.351 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_components.py:

diff --git a/main/_sources/tutorials/phasorpy_fret.rst.txt b/main/_sources/tutorials/phasorpy_fret.rst.txt
@@ -407,7 +407,7 @@ mypy: disable-error-code="arg-type"
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.684 seconds)
+   **Total running time of the script:** (0 minutes 1.687 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_fret.py:

diff --git a/main/_sources/tutorials/phasorpy_introduction.rst.txt b/main/_sources/tutorials/phasorpy_introduction.rst.txt
@@ -424,14 +424,14 @@ Print information about Python interpreter and installed packages:
     Python-3.11.9
     phasorpy-0.1.dev
     numpy-2.0.0
-    tifffile-2024.5.22
+    tifffile-2024.6.18
     imagecodecs-n/a
     lfdfiles-2024.5.24
     sdtfile-2024.5.24
     ptufile-2024.5.24
     matplotlib-3.9.0
-    scipy-1.13.1
-    skimage-0.23.2
+    scipy-1.14.0
+    skimage-0.24.0
     sklearn-n/a
     pandas-2.2.2
     xarray-2024.6.0
@@ -448,7 +448,7 @@ sphinx_gallery_thumbnail_number = 3
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 8.227 seconds)
+   **Total running time of the script:** (0 minutes 11.222 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_introduction.py:

diff --git a/main/_sources/tutorials/phasorpy_phasor_from_lifetime.rst.txt b/main/_sources/tutorials/phasorpy_phasor_from_lifetime.rst.txt
@@ -358,7 +358,7 @@ sphinx_gallery_thumbnail_number = -2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.447 seconds)
+   **Total running time of the script:** (0 minutes 0.445 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_phasor_from_lifetime.py:

diff --git a/main/_sources/tutorials/sg_execution_times.rst.txt b/main/_sources/tutorials/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:11.378** total execution time for 5 files **from tutorials**:
+**00:14.374** total execution time for 5 files **from tutorials**:
 
 .. container::
 
@@ -33,17 +33,17 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_phasorpy_introduction.py` (``phasorpy_introduction.py``)
-     - 00:08.227
+     - 00:11.222
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_fret.py` (``phasorpy_fret.py``)
-     - 00:01.684
+     - 00:01.687
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasorplot.py` (``phasorpy_phasorplot.py``)
      - 00:00.669
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasor_from_lifetime.py` (``phasorpy_phasor_from_lifetime.py``)
-     - 00:00.447
+     - 00:00.445
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_components.py` (``phasorpy_components.py``)
-     - 00:00.350
+     - 00:00.351
      - 0.0