{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "ExecuteTime": { "end_time": "2019-02-26T18:49:24.117386Z", "start_time": "2019-02-26T18:49:24.076329Z" } }, "outputs": [], "source": [ "# for automatic reloading\n", "%load_ext autoreload\n", "%autoreload 2" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "ExecuteTime": { "end_time": "2019-02-26T18:49:26.950567Z", "start_time": "2019-02-26T18:49:24.651822Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/mnt/cube/tsainbur/conda_envs/tpy3/lib/python3.6/site-packages/tqdm/autonotebook/__init__.py:14: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n", " \" (e.g. in jupyter console)\", TqdmExperimentalWarning)\n" ] } ], "source": [ "from birdbrain.atlas import atlas\n", "import numpy as np" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "ExecuteTime": { "end_time": "2019-02-26T18:55:11.181582Z", "start_time": "2019-02-26T18:55:11.126077Z" } }, "outputs": [], "source": [ "from birdbrain.utils import um_to_vox, vox_to_um" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "ExecuteTime": { "end_time": "2019-02-26T18:49:29.040802Z", "start_time": "2019-02-26T18:49:28.983193Z" } }, "outputs": [], "source": [ "from birdbrain.visualization.plotting_2d import plot_2d_coordinates" ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "ExecuteTime": { "end_time": "2019-02-26T19:02:50.397719Z", "start_time": "2019-02-26T19:02:48.274614Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Data already download\n", "Getting voxel data from .img files...\n", "Getting location for each nucleus/region from voxel data...\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "", "version_major": 2, "version_minor": 0 }, "text/plain": [ "HBox(children=(IntProgress(value=0, max=41), HTML(value='')))" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\r", "Atlas created\n" ] } ], "source": [ "dset_dir = '../../data/processed/mustached_bat/'\n", "\n", "mustached_bat_atlas = atlas(\n", " species = 'mustached_bat',\n", " dset_dir = dset_dir,\n", " um_mult = 1000,\n", " smoothing = []#['Brain', 'Brainregions']\n", ")" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "ExecuteTime": { "end_time": "2019-02-26T19:02:50.877124Z", "start_time": "2019-02-26T19:02:50.824478Z" } }, "outputs": [ { "data": { "text/html": [ "
| \n", " | label | \n", "region | \n", "type_ | \n", "
|---|---|---|---|
| region | \n", "\n", " | \n", " | \n", " |
| Exterior | \n", "1 | \n", "Exterior | \n", "Mustached_bat_delineations | \n", "
| Inferior.Colliculus_IC | \n", "2 | \n", "Inferior.Colliculus_IC | \n", "Mustached_bat_delineations | \n", "
| Commissure.of.Inferior.Colliculus_cic | \n", "3 | \n", "Commissure.of.Inferior.Colliculus_cic | \n", "Mustached_bat_delineations | \n", "