From 09731da4be4b85474beb54a26a94383d50560c9c Mon Sep 17 00:00:00 2001 From: Carsen Stringer Date: Wed, 16 Oct 2024 12:19:42 -0400 Subject: [PATCH] updating notebook params --- notebooks/rastermap_largescale.ipynb | 3 +-- notebooks/rastermap_singleneurons.ipynb | 6 +++--- paper/fig4.ipynb | 4 ++-- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/notebooks/rastermap_largescale.ipynb b/notebooks/rastermap_largescale.ipynb index a960ce7..188e8d0 100644 --- a/notebooks/rastermap_largescale.ipynb +++ b/notebooks/rastermap_largescale.ipynb @@ -103,8 +103,7 @@ "source": [ "model = Rastermap(n_clusters=100, # number of clusters to compute\n", " n_PCs=128, # number of PCs to use\n", - " locality=0.75, # locality in sorting to find sequences (this is a value from 0-1)\n", - " time_lag_window=5, # use future timepoints to compute correlation\n", + " locality=0., # locality in sorting to find sequences (this is a value from 0-1)\n", " grid_upsample=10, # default value, 10 is good for large recordings\n", " ).fit(spks)\n", "y = model.embedding # neurons x 1\n", diff --git a/notebooks/rastermap_singleneurons.ipynb b/notebooks/rastermap_singleneurons.ipynb index bfa4bd8..fd24da5 100644 --- a/notebooks/rastermap_singleneurons.ipynb +++ b/notebooks/rastermap_singleneurons.ipynb @@ -27,7 +27,7 @@ "outputs": [], "source": [ "!pip install numpy>=1.24 # (required for google colab)\n", - "!pip install rastermap \n", + "!pip install rastermap\n", "!pip install matplotlib" ] }, @@ -95,7 +95,7 @@ "source": [ "model = Rastermap(n_clusters=None, # None turns off clustering and sorts single neurons \n", " n_PCs=64, # use fewer PCs than neurons\n", - " locality=0.15, # some locality in sorting (this is a value from 0-1)\n", + " locality=0.1, # some locality in sorting (this is a value from 0-1)\n", " time_lag_window=15, # use future timepoints to compute correlation\n", " grid_upsample=0, # 0 turns off upsampling since we're using single neurons\n", " ).fit(spks)\n", @@ -255,7 +255,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.10" + "version": "3.9.16" }, "orig_nbformat": 4, "vscode": { diff --git a/paper/fig4.ipynb b/paper/fig4.ipynb index a59a835..739f539 100644 --- a/paper/fig4.ipynb +++ b/paper/fig4.ipynb @@ -63,8 +63,8 @@ "\n", "model = Rastermap(n_clusters=None, \n", " n_PCs=64, \n", - " locality=0.1, # 0.1<-include nan's, #0.05 <- interp nan's #0.25 <- remove nan's\n", - " time_lag_window=15, # 15<- include nan's, #10 <- interp nan's # 20 <- remove nan's\n", + " locality=0.1, \n", + " time_lag_window=15, \n", " symmetric=False,\n", " grid_upsample=0,\n", " ).fit(spks)\n",