diff --git a/atlas-analysis.ipynb b/atlas-analysis.ipynb
new file mode 100644
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@@ -0,0 +1,1827 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "id": "f6ebd680",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import plotly.express as px\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "085ecf02",
+ "metadata": {},
+ "source": [
+ "There is currently a bug in imaris:\n",
+ "intensity values are rounded after the 6th digit, but the allen brain atlas contains higher values then this, at least 9 digits. There are several different 9 digit values in the atlas, which would all get rounded to the same 6 digit value...\n",
+ "hence, we remapped the atlas label image and need to undo said remapping again now."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "id": "31cef6ca",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# There is a \"0\" label in the original atlas, and it gets lost when remapping in ImageJ.\n",
+ "# However, it labels \"outside\" the atlas, so we could also just ignor it.\n",
+ "# Could also be added manually to the dataframe or in IJ."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "id": "689bbcf3",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# read the relevant files\n",
+ "\n",
+ "imaris_result = \"./DOE020951_RC_Tile0_Ch561_Sh0_downsampled_32bit_atlaschannel_remapped_Detailed.csv\"\n",
+ "atlas_remapping = \"./registered_atlas_original_orientation_rotated_labelmap.csv\" # Imaris bug workaround\n",
+ "atlas_structures = \"./structures.csv\"\n",
+ "\n",
+ "df_imaris_result = pd.read_csv(imaris_result, header=2)\n",
+ "df_atlas_remapping = pd.read_csv(atlas_remapping, header=0)\n",
+ "df_atlas_structures = pd.read_csv(atlas_structures, header=0)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "id": "346f07ee",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>Intensity Center</th>\n",
+ " <th>Unit</th>\n",
+ " <th>Category</th>\n",
+ " <th>Channel</th>\n",
+ " <th>Image</th>\n",
+ " <th>Time</th>\n",
+ " <th>ID</th>\n",
+ " <th>Unnamed: 7</th>\n",
+ " <th>original labels</th>\n",
+ " <th>remapped labels</th>\n",
+ " <th>acronym</th>\n",
+ " <th>id</th>\n",
+ " <th>name</th>\n",
+ " <th>structure_id_path</th>\n",
+ " <th>parent_structure_id</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>419</td>\n",
+ " <td>NaN</td>\n",
+ " <td>Spot</td>\n",
+ " <td>3</td>\n",
+ " <td>Image 1</td>\n",
+ " <td>1</td>\n",
+ " <td>36</td>\n",
+ " <td>NaN</td>\n",
+ " <td>844.0</td>\n",
+ " <td>419.0</td>\n",
+ " <td>MOp6a</td>\n",
+ " <td>844.0</td>\n",
+ " <td>Primary motor area, Layer 6a</td>\n",
+ " <td>/997/8/567/688/695/315/500/985/844/</td>\n",
+ " <td>985.0</td>\n",
+ " </tr>\n",
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+ " <td>1</td>\n",
+ " <td>371</td>\n",
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+ " <td>844.0</td>\n",
+ " <td>419.0</td>\n",
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+ " <td>1</td>\n",
+ " <td>495</td>\n",
+ " <td>NaN</td>\n",
+ " <td>844.0</td>\n",
+ " <td>419.0</td>\n",
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+ " <td>844.0</td>\n",
+ " <td>Primary motor area, Layer 6a</td>\n",
+ " <td>/997/8/567/688/695/315/500/985/844/</td>\n",
+ " <td>985.0</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>468</td>\n",
+ " <td>NaN</td>\n",
+ " <td>Spot</td>\n",
+ " <td>3</td>\n",
+ " <td>Image 1</td>\n",
+ " <td>1</td>\n",
+ " <td>808</td>\n",
+ " <td>NaN</td>\n",
+ " <td>940.0</td>\n",
+ " <td>468.0</td>\n",
+ " <td>cing</td>\n",
+ " <td>940.0</td>\n",
+ " <td>cingulum bundle</td>\n",
+ " <td>/997/1009/991/768/940/</td>\n",
+ " <td>768.0</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>...</th>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>13604</th>\n",
+ " <td>38</td>\n",
+ " <td>NaN</td>\n",
+ " <td>Spot</td>\n",
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+ " <td>1518152</td>\n",
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+ " <td>78.0</td>\n",
+ " <td>38.0</td>\n",
+ " <td>mcp</td>\n",
+ " <td>78.0</td>\n",
+ " <td>middle cerebellar peduncle</td>\n",
+ " <td>/997/1009/960/752/78/</td>\n",
+ " <td>752.0</td>\n",
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+ " <td>sV</td>\n",
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+ " <td>sensory root of the trigeminal nerve</td>\n",
+ " <td>/997/1009/967/901/229/</td>\n",
+ " <td>901.0</td>\n",
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+ " <tr>\n",
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+ " <td>117</td>\n",
+ " <td>NaN</td>\n",
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+ " <td>Image 1</td>\n",
+ " <td>1</td>\n",
+ " <td>1518488</td>\n",
+ " <td>NaN</td>\n",
+ " <td>229.0</td>\n",
+ " <td>117.0</td>\n",
+ " <td>sV</td>\n",
+ " <td>229.0</td>\n",
+ " <td>sensory root of the trigeminal nerve</td>\n",
+ " <td>/997/1009/967/901/229/</td>\n",
+ " <td>901.0</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>13609 rows × 15 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " Intensity Center Unit Category Channel Image Time ID \\\n",
+ "0 419 NaN Spot 3 Image 1 1 36 \n",
+ "1 419 NaN Spot 3 Image 1 1 168 \n",
+ "2 419 NaN Spot 3 Image 1 1 371 \n",
+ "3 419 NaN Spot 3 Image 1 1 495 \n",
+ "4 468 NaN Spot 3 Image 1 1 808 \n",
+ "... ... ... ... ... ... ... ... \n",
+ "13604 38 NaN Spot 3 Image 1 1 1518152 \n",
+ "13605 38 NaN Spot 3 Image 1 1 1518156 \n",
+ "13606 38 NaN Spot 3 Image 1 1 1518261 \n",
+ "13607 117 NaN Spot 3 Image 1 1 1518478 \n",
+ "13608 117 NaN Spot 3 Image 1 1 1518488 \n",
+ "\n",
+ " Unnamed: 7 original labels remapped labels acronym id \\\n",
+ "0 NaN 844.0 419.0 MOp6a 844.0 \n",
+ "1 NaN 844.0 419.0 MOp6a 844.0 \n",
+ "2 NaN 844.0 419.0 MOp6a 844.0 \n",
+ "3 NaN 844.0 419.0 MOp6a 844.0 \n",
+ "4 NaN 940.0 468.0 cing 940.0 \n",
+ "... ... ... ... ... ... \n",
+ "13604 NaN 78.0 38.0 mcp 78.0 \n",
+ "13605 NaN 78.0 38.0 mcp 78.0 \n",
+ "13606 NaN 78.0 38.0 mcp 78.0 \n",
+ "13607 NaN 229.0 117.0 sV 229.0 \n",
+ "13608 NaN 229.0 117.0 sV 229.0 \n",
+ "\n",
+ " name \\\n",
+ "0 Primary motor area, Layer 6a \n",
+ "1 Primary motor area, Layer 6a \n",
+ "2 Primary motor area, Layer 6a \n",
+ "3 Primary motor area, Layer 6a \n",
+ "4 cingulum bundle \n",
+ "... ... \n",
+ "13604 middle cerebellar peduncle \n",
+ "13605 middle cerebellar peduncle \n",
+ "13606 middle cerebellar peduncle \n",
+ "13607 sensory root of the trigeminal nerve \n",
+ "13608 sensory root of the trigeminal nerve \n",
+ "\n",
+ " structure_id_path parent_structure_id \n",
+ "0 /997/8/567/688/695/315/500/985/844/ 985.0 \n",
+ "1 /997/8/567/688/695/315/500/985/844/ 985.0 \n",
+ "2 /997/8/567/688/695/315/500/985/844/ 985.0 \n",
+ "3 /997/8/567/688/695/315/500/985/844/ 985.0 \n",
+ "4 /997/1009/991/768/940/ 768.0 \n",
+ "... ... ... \n",
+ "13604 /997/1009/960/752/78/ 752.0 \n",
+ "13605 /997/1009/960/752/78/ 752.0 \n",
+ "13606 /997/1009/960/752/78/ 752.0 \n",
+ "13607 /997/1009/967/901/229/ 901.0 \n",
+ "13608 /997/1009/967/901/229/ 901.0 \n",
+ "\n",
+ "[13609 rows x 15 columns]"
+ ]
+ },
+ "execution_count": 31,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# merge tables / remap to work around the Imaris bug\n",
+ "# \"ID\" refers to imaris spots , \"id\" refers to the allen atlas\n",
+ "\n",
+ "df_temp = pd.merge(df_imaris_result, df_atlas_remapping, left_on=\"Intensity Center\", right_on=\"remapped labels\", how = \"left\")\n",
+ "combined_results = pd.merge(df_temp, df_atlas_structures, left_on=\"original labels\", right_on=\"id\", how = \"left\")\n",
+ "combined_results"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "id": "e081270f",
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "data": {
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+ "VL 2307\n",
+ "CP 2011\n",
+ "stc 1862\n",
+ "SEZ 517\n",
+ "ccg 322\n",
+ "DG-sg 291\n",
+ "root 289\n",
+ "fi 225\n",
+ "STR 223\n",
+ "SI 213\n",
+ "fp 174\n",
+ "LSr 166\n",
+ "HY 152\n",
+ "V3 149\n",
+ "DG-po 146\n",
+ "LHA 135\n",
+ "MB 128\n",
+ "BST 119\n",
+ "LSv 116\n",
+ "DG-mo 103\n",
+ "ACB 102\n",
+ "CA3 96\n",
+ "LSc 90\n",
+ "fiber tracts 90\n",
+ "aco 88\n",
+ "ccs 86\n",
+ "cpd 80\n",
+ "chpl 80\n",
+ "ZI 79\n",
+ "alv 78\n",
+ "Name: acronym, dtype: int64"
+ ]
+ },
+ "execution_count": 33,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# aggregate the occurence of a given label\n",
+ "\n",
+ "int_value_counts = combined_results[\"acronym\"].value_counts() # is ordered by highest occurance first\n",
+ "\n",
+ "index_values = int_value_counts.index.tolist()\n",
+ "counts = int_value_counts.values\n",
+ "\n",
+ "# show just the first 30 values.\n",
+ "int_value_counts.iloc[:30]\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 34,
+ "id": "219cbba2",
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