{
"cells": [
{
"cell_type": "markdown",
"id": "d22a9306",
"metadata": {},
"source": [
"# Probes\n",
"[](https://colab.research.google.com/github/VirtualBrainLab/urchin-examples/blob/main/basics/probes.ipynb)"
]
},
{
"cell_type": "markdown",
"id": "ac0754d0",
"metadata": {},
"source": [
"## Install Urchin\n",
"\n",
"Urchin is a Python package stored on PyPI, the following code needs to be run the first time you use Urchin in a Python environment. \n",
"\n",
"Urchin's full documentation can be found [on our website](https://virtualbrainlab.org/urchin/installation_and_use.html)."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8f04ec05",
"metadata": {},
"outputs": [],
"source": [
"#Installing urchin\n",
"!pip install oursin -U\n",
"\n",
"# Pandas also required for this tutorial\n",
"!pip install pandas"
]
},
{
"cell_type": "markdown",
"id": "d359d23b",
"metadata": {},
"source": [
"## Setup Urchin and open the renderer webpage \n",
"\n",
"By default Urchin opens the 3D renderer in a webpage. Make sure pop-ups are enabled, or the page won't open properly. You can also open the renderer site yourself by replacing [ID here] with the ID that is output by the call to `.setup()` at https://data.virtualbrainlab.org/Urchin/?ID=[ID here]\n",
"\n",
"Note that Urchin communicates to the renderer webpage through an internet connection, we don't currently support offline use (we hope to add support in the future)."
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "b384b2b7",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(URN) connected to server\n",
"Login sent with ID: 0d284442, copy this ID into the renderer to connect.\n"
]
}
],
"source": [
"#Importing necessary libraries:\n",
"import oursin as urchin\n",
"import pandas as pd\n",
"urchin.setup()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Download data\n",
"For this tutorial, let's explore the dataset from [Steinmetz et al. 2019](https://www.nature.com/articles/s41586-019-1787-x). We'll get the position of all the insertions and then display them within a 3D mesh of the brain, recreating figure 1h.\n",
"\n",
""
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"# Define a quick convenience function for loading data\n",
"def get_data(url):\n",
" data = url.replace(\"/edit#gid=\", \"/export?format=csv&gid=\")\n",
" df = pd.read_csv(data)\n",
" return df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The angles in the original dataset also need to be rotated to match the conventions in Urchin."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"probe_data = get_data('https://docs.google.com/spreadsheets/d/1T-RG3d_MIBXZKmrGmLnsU-O7GmwY09Z0FY6yqbYyZXI/edit#gid=1457359713')\n",
"probe_data[\"theta\"] = 90 - probe_data[\"theta\"]\n",
"probe_data[\"phi\"] = 270 - probe_data[\"phi\"] "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Data overview\n",
"ML, AP, and DV, refer to the coordinates of the tip of the probe along the medial-lateral, anterior-posterior, and dorsal-ventral axes, within the CCF coordinate space. The phi and theta angles correspond to yaw (azimuth) and pitch (elevation) in Urchin."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
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