add n5_download_demo.ipynb similar to ImageJ download using tensorstore

Author: jcschaff

examples/n5_download_demo.ipynb

@@ -0,0 +1,102 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# reading an exported VCell dataset from a server-side N5 store\n",
+    "1. set up tensorstore to point to remote dataset\n",
+    "2. retrieve data as a datastore object which lazily loads data upon request."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "29a6cffd5df3cb63"
+  },
+  {
+   "cell_type": "code",
+   "source": "import tensorstore as ts",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-24T00:55:40.251947Z",
+     "start_time": "2025-01-24T00:55:39.504432Z"
+    }
+   },
+   "id": "c94978b833082ef7",
+   "outputs": [],
+   "execution_count": 1
+  },
+  {
+   "cell_type": "markdown",
+   "source": "### this configuration can be simplified by wrapping in pyvcell library",
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "4b69965b59dd9af5"
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "# Define the URL and dataset name\n",
+    "url = \"https://vcell.cam.uchc.edu/n5Data/ACowan/11a0e2db531a208.n5\"\n",
+    "dataset_name = \"5580791597\"\n",
+    "\n",
+    "# Open the N5 dataset\n",
+    "spec = {\n",
+    "    \"driver\": \"n5\",\n",
+    "    \"kvstore\": {\n",
+    "        \"driver\": \"http\",\n",
+    "        \"base_url\": url\n",
+    "    },\n",
+    "    \"path\": dataset_name\n",
+    "}\n",
+    "\n",
+    "# Read the specified dataset\n",
+    "dataset = ts.open(spec).result()\n",
+    "data = dataset.read().result()\n",
+    "\n",
+    "# Print the shape of the data\n",
+    "print(\"Data shape:\", data.shape)\n"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-24T00:56:05.521770Z",
+     "start_time": "2025-01-24T00:55:49.489764Z"
+    }
+   },
+   "id": "e88a4bb558aba920",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Data shape: (51, 51, 2, 51, 103)\n"
+     ]
+    }
+   ],
+   "execution_count": 2
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

scripts/run_notebook.sh

@@ -8,6 +8,6 @@ cd ${ROOT_DIR} || (echo "Failed to cd into ${ROOT_DIR}" && exit 1)
 
 python -m venv .venv_jupyter
 source .venv_jupyter/bin/activate
-pip install jupyter ipython matplotlib
+pip install jupyter ipython matplotlib tensorstore
 poetry install
 jupyter notebook