{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Extracellular Electrophysiology Data Quick Start\n", "\n", "A short introduction to the Visual Coding Neuropixels data and SDK. For more information, see the full reference notebook.\n", "\n", "Contents\n", "-------------\n", "* peristimulus time histograms\n", "* image decoding" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import os\n", "\n", "import numpy as np\n", "import pandas as pd\n", "import matplotlib.pyplot as plt\n", "\n", "from allensdk.brain_observatory.ecephys.ecephys_project_cache import EcephysProjectCache" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The `EcephysProjectCache` is the main entry point to the Visual Coding Neuropixels dataset. It allows you to download data for individual recording sessions and view cross-session summary information." ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['brain_observatory_1.1', 'functional_connectivity']\n" ] } ], "source": [ "# this path determines where downloaded data will be stored\n", "manifest_path = os.path.join(\"example_ecephys_project_cache\", \"manifest.json\")\n", "\n", "cache = EcephysProjectCache.from_warehouse(manifest=manifest_path)\n", "\n", "print(cache.get_all_session_types())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This dataset contains sessions in which two sets of stimuli were presented. The `\"brain_observatory_1.1\"` sessions are (almost exactly) the same as Visual Coding 2P sessions." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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797828357 | \n", "2019-01-08T21:26:13Z | \n", "787643635 | \n", "2019-10-03T00:00:00Z | \n", "776061251 | \n", "brain_observatory_1.1 | \n", "107.0 | \n", "M | \n", "Pvalb-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt | \n", "611 | \n", "2232 | \n", "6 | \n", "[PPT, MB, APN, NOT, HPF, ProS, CA1, VISam, nan... | \n", "
798911424 | \n", "2018-12-21T08:02:57Z | \n", "785726931 | \n", "2019-10-03T00:00:00Z | \n", "775876828 | \n", "brain_observatory_1.1 | \n", "110.0 | \n", "F | \n", "Vip-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt | \n", "825 | \n", "2233 | \n", "6 | \n", "[APN, TH, Eth, LP, DG, HPF, CA3, CA1, VISrl, n... | \n", "
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