{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Cell Specimen Mapping\n",
"The cross-session alignment algorithm has been updated and re-run just prior to release 0.13.2 (June 15th, 2017). As a result all cell specimen IDs have changed. We have built a mapping table to help map from previous cell IDs to new cell IDs. The table is available as a `WellKnownFile` and the `BrainObservatoryApi` provides a method for downloading it and loading it as a DataFrame.\n",
"\n",
"Download this file in .ipynb format here."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Downloading the Mapping Table\n",
"The `BrainObservatoryApi` provides a `get_cell_specimen_id_mapping` method for downloading the mapping table as a CSV file. The method requires a file name to save the table to, and will return the table as a DataFrame."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"RangeIndex: 27124 entries, 0 to 27123\n",
"Data columns (total 4 columns):\n",
"old_cell_id 27124 non-null int64\n",
"session_A_new_cell_id 18492 non-null float64\n",
"session_B_new_cell_id 17674 non-null float64\n",
"session_C_new_cell_id 16868 non-null float64\n",
"dtypes: float64(3), int64(1)\n",
"memory usage: 847.7 KB\n"
]
}
],
"source": [
"from allensdk.api.queries.brain_observatory_api import BrainObservatoryApi\n",
"\n",
"api = BrainObservatoryApi()\n",
"\n",
"table = api.get_cell_specimen_id_mapping(\"./cell_mapping_table.csv\")\n",
"\n",
"table.info()"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"## Using the Mapping Table\n",
"The cell specimen mapping table contains 4 columns, `old_cell_id`, `session_A_new_cell_id`, `session_B_new_cell_id`, `session_C_new_cell_id`. In some instances, multiple ROIs that were assigned to a single cell specimen may now be considered distinct cells after reprocessing, so an old cell specimen ID may map to different cell specimens in different sessions."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
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