diff --git a/experiments/BrainLine/axon_analysis.ipynb b/experiments/BrainLine/axon_analysis.ipynb index 36fb6767..2cc71dd4 100644 --- a/experiments/BrainLine/axon_analysis.ipynb +++ b/experiments/BrainLine/axon_analysis.ipynb @@ -10,7 +10,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -79,17 +79,9 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Path to brainlit: /home/user/brainlit\n" - ] - } - ], + "outputs": [], "source": [ "brainlit_path = Path(os.path.abspath(\"\"))\n", "brainlit_path = brainlit_path.parents[1]\n", @@ -628,7 +620,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -703,2428 +695,23 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": null, "metadata": {}, - "outputs": [ - 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This is discouraged.\n", - "Gtk-Message: 17:31:18.922: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:31:33.145: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:31:47.615: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:32:03.530: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:32:17.742: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:32:32.294: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:32:47.741: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:33:02.775: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:33:17.784: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:33:31.184: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:33:44.621: GtkDialog mapped without a transient parent. This is discouraged.\n" - ] - } - ], + "outputs": [], "source": [ "dir = \"/home/user/misc_tommy/figures/axon_coronal/\"\n", "z_size = 1300\n", @@ -3147,49 +734,9 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Downloading transformed_mask from brain: MS15\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Downloading: 100%|██████████| 37800/37800 [03:27<00:00, 182.01it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(1140, 800, 1320)\n", - "(1140, 800, 1320)\n" - ] - }, - { - "data": { - "text/html": [ - "
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-       "Saving new screenshot at brainrender_screenshot_20241211_154317.png\n",
-       "\n",
-       "
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"execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -89,17 +89,9 @@ }, { "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Path to brainlit: {brainlit_path}\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "brainlit_path = Path(os.path.abspath(\"\"))\n", "brainlit_path = brainlit_path.parents[1]\n", @@ -645,171 +637,9 @@ }, { "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Brain 8557: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8557/transformed_points.json\n", - "Brain 8555: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8555/transformed_points.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points0.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points6.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points2.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points5.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points3.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points4.json\n", - "Brain 8607: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8607/transformed_points1.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points0.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points11.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points10.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points9.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points6.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points8.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points2.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points7.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points5.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points3.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points4.json\n", - "Brain 8606: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8606/transformed_points1.json\n", - "Brain 8608: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8608/transformed_points.json\n", - "Brain MPRRabies: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MPRRabies/transformed_points.json\n", - "Brain 969: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_969/transformed_points0.json\n", - "Brain 969: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_969/transformed_points1.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points0.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points10.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points9.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points6.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points8.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points2.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points7.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points5.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points3.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points4.json\n", - "Brain 892: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_892/transformed_points1.json\n", - "Brain MS37: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS37/transformed_points.json\n", - "Brain MS36: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS36/transformed_points.json\n", - "Brain MS25_v2: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS25_v2/transformed_points0.json\n", - "Brain MS25_v2: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS25_v2/transformed_points1.json\n", - "Brain MS23: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS23/transformed_points.json\n", - "Brain MS22: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS22/transformed_points.json\n", - "Brain MS50_v2: Collecting atlas space soma points from layer: transformed_points\n", - "Brain MS39: Collecting atlas space soma points from layer: transformed_points\n", - "Brain MS21: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS21/transformed_points0.json\n", - "Brain MS21: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_MS21/transformed_points1.json\n", - "Brain 1252B: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_1252B/transformed_points.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points12.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points0.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points11.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points15.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points10.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points9.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points6.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points8.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points14.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points17.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points13.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points2.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points7.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points5.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points3.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points16.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points4.json\n", - "Brain 8030R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_8030R/transformed_points1.json\n", - "Brain 5573N: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_5573N/transformed_points0.json\n", - "Brain 5573N: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_5573N/transformed_points2.json\n", - "Brain 5573N: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_5573N/transformed_points3.json\n", - "Brain 5573N: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_5573N/transformed_points1.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points0.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points6.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points2.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points7.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points5.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points3.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points4.json\n", - "Brain 21260L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260L/transformed_points1.json\n", - "Brain 21260B: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260B/transformed_points0.json\n", - "Brain 21260B: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260B/transformed_points2.json\n", - "Brain 21260B: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260B/transformed_points1.json\n", - "Brain 21260R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260R/transformed_points0.json\n", - "Brain 21260R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260R/transformed_points2.json\n", - "Brain 21260R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260R/transformed_points3.json\n", - "Brain 21260R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260R/transformed_points4.json\n", - "Brain 21260R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21260R/transformed_points1.json\n", - "Brain 21268N: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21268N/transformed_points0.json\n", - "Brain 21268N: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_21268N/transformed_points1.json\n", - "Brain 38035L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_38035L/transformed_points0.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points12.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points0.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points11.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points15.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points10.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points9.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points6.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points19.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points8.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points14.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points20.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points17.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points18.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points13.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points21.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points2.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points7.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points5.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points3.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points16.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points4.json\n", - "Brain 274L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_274L/transformed_points1.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points12.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points0.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points11.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points15.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points10.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points9.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points6.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points19.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points8.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points14.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points25.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points22.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points20.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points17.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points18.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points13.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points21.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points2.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points7.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points5.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points3.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points16.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points24.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points4.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points23.json\n", - "Brain 257R: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_257R/transformed_points1.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points0.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points9.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points6.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points8.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points2.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points7.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points5.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points3.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points4.json\n", - "Brain 028L: Collecting atlas space soma points from file: /home/user/brainlit/experiments/BrainLine/data/wholebrain-results/soma/atlas_somas_028L/transformed_points1.json\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Finding soma regions of brains: 100%|██████████| 27/27 [00:04<00:00, 5.53it/s]\n", - "Finding soma regions of brains: 100%|██████████| 27/27 [00:04<00:00, 5.73it/s]\n", - "Finding soma regions of brains: 100%|██████████| 27/27 [00:04<00:00, 5.53it/s]\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "brain_ids = [\n", " \"8557\", # before aug 2022,\n", @@ -908,67 +738,9 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Relabeling slice: 100%|██████████| 21/21 [00:00<00:00, 1291.61it/s]\n", - "Processing labels: 100%|██████████| 13/13 [00:00<00:00, 98.76it/s] \n", - "Processing brains in z=200: 100%|██████████| 27/27 [00:01<00:00, 15.63it/s]\n", - "Relabeling slice: 100%|██████████| 46/46 [00:00<00:00, 1466.55it/s]\n", - "Processing labels: 100%|██████████| 6/6 [00:00<00:00, 106.71it/s]\n", - "Processing brains in z=300: 100%|██████████| 27/27 [00:01<00:00, 15.02it/s]\n", - "Relabeling slice: 100%|██████████| 67/67 [00:00<00:00, 1552.50it/s]\n", - 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"100%|██████████| 11/11 [02:32<00:00, 13.83s/it]\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Gtk-Message: 17:49:14.039: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:49:34.469: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:50:02.705: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:50:19.551: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:50:35.523: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:50:51.916: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:51:07.673: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:51:22.497: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:51:36.511: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:51:51.279: GtkDialog mapped without a transient parent. This is discouraged.\n", - "Gtk-Message: 17:52:04.594: GtkDialog mapped without a transient parent. This is discouraged.\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "dir = \"/Users/thomasathey/Documents/mimlab/mouselight/ailey/matt-coronals/\"\n", "z_size = 1320\n", @@ -994,84 +766,9 @@ }, { "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Skipping IndexError exception while plotting points in brainrender: index 268 is out of bounds for axis 0 with size 264\n", - "Skipping IndexError exception while plotting points in brainrender: index 165 is out of bounds for axis 1 with size 160\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Skipping IndexError exception while plotting points in brainrender: index 268 is out of bounds for axis 0 with size 264\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Skipping IndexError exception while plotting points in brainrender: index 264 is out of bounds for axis 0 with size 264\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "028L - 9978 points\n" - ] - }, - { - "data": { - "text/html": [ - "
\n",
-       "Saving new screenshot at brainrender_screenshot_20241211_160755.png\n",
-       "\n",
-       "
\n" - ], - "text/plain": [ - "\n", - "Saving new screenshot at brainrender_screenshot_20241211_160755.png\n", - "\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "sd.brainrender_somas(subtype_colors=colors)" ] @@ -1420,7 +1117,7 @@ "metadata": {}, "outputs": [], "source": [ - "regions_exc = regions_coarse_part\n", + "regions_exc = regions_coarse_part_weiss\n", "\n", "for r_src in regions_exc:\n", " # print(sd.region_graph.nodes[r_src][\"name\"])\n", @@ -1731,7 +1428,7 @@ "\n", "fig.tight_layout()\n", "#plt.show()\n", - "plt.savefig('/home/user/misc_tommy/figures/soma_barplot/barplot.svg')\n", + "#plt.savefig('/home/user/misc_tommy/figures/soma_barplot/barplot.svg')\n", "#df.to_csv(\"/home/user/misc_tommy/figures/soma_barplot/data.csv\")" ] }, @@ -1751,7 +1448,7 @@ "metadata": {}, "outputs": [], "source": [ - "regions = regions_coarse_part\n", + "regions = regions_coarse_part_weiss\n", "composite_region = {}\n", "\n", "pad=1\n", @@ -1926,10 +1623,12 @@ " df_means.append(mean)\n", " df_subtypes.append(subtype)\n", "\n", - "data = {\"Mean\": df_means, \"Subtype\": df_subtypes, \"Region\": df_regions}\n", + "data = {\"ILR Mean Fraction of Inputs\": df_means, \"Subtype\": df_subtypes, \"Region\": df_regions}\n", "\n", - "sns.barplot(x=\"Mean\", y=\"Region\", hue=\"Subtype\", data=pd.DataFrame(data=data))\n", - "plt.show()" + "sns.barplot(x=\"ILR Mean Fraction of Inputs\", y=\"Region\", hue=\"Subtype\", palette=color_palette, data=pd.DataFrame(data=data))\n", + "\n", + "plt.savefig(\"/home/user/misc_tommy/figures/pca/means_soma.svg\", format=\"svg\")\n", + "#plt.show()" ] }, { @@ -1970,14 +1669,14 @@ "\n", "\n", "fig, ax = plt.subplots(1, 1, figsize=(8, 6), dpi=300)\n", - "ax = sns.scatterplot(x=pc1_lbl, y=pc2_lbl, hue=\"Subtype\", data=df, ax=ax)\n", + "ax = sns.scatterplot(x=pc1_lbl, y=pc2_lbl, hue=\"Subtype\", palette=color_palette, data=df, ax=ax)\n", "# for i, row in df.iterrows():\n", "# ax.text(row[pc1_lbl], row[pc2_lbl], row[\"ID\"], rotation=45)\n", "\n", "# ax.set_xlim(-1.5, -0.5)\n", "# ax.set_ylim(-1.5, -0.5)\n", - "plt.show()\n", - "#plt.savefig(\"/Users/thomasathey/Desktop/test.svg\", format=\"svg\")" + "#plt.show()\n", + "plt.savefig(\"/home/user/misc_tommy/figures/pca/pca_soma.svg\", format=\"svg\")" ] }, {