demo of panel-neuroglancer

panel_neuroglancer_demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "dc9888ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "# /// script\n",
    "# requires-python = \">=3.10\"\n",
    "# dependencies = [\n",
    "#     \"panel-neuroglancer\",\n",
    "# ]\n",
    "# ///"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5b7c37cb",
   "metadata": {},
   "outputs": [],
   "source": [
    "from panel_neuroglancer import Neuroglancer\n",
    "import neuroglancer\n",
    "import panel as pn\n",
    "pn.extension()\n",
    "\n",
    "viewer = neuroglancer.Viewer()\n",
    "\n",
    "with viewer.txn() as s:\n",
    "    s.layers[\"em\"] = neuroglancer.ImageLayer(\n",
    "        source=\"zarr://s3://janelia-cosem-datasets/jrc_mus-kidney-3/jrc_mus-kidney-3.zarr/recon-1/em/fibsem-uint8/\",\n",
    "    )\n",
    "    # Add a segmentation layer\n",
    "    s.layers[\"segmentation\"] = neuroglancer.SegmentationLayer(\n",
    "        source=\"zarr://s3://janelia-cosem-datasets/jrc_mus-kidney-3/jrc_mus-kidney-3.zarr/recon-1/labels/inference/segmentations/nuc/\",\n",
    "    )\n",
    "Neuroglancer(source=viewer, show_state=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c20bb280-0ba0-4378-9119-f25e5ccd4bb8",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}