diff --git a/docs/notebooks/widget_segmentations_beta.ipynb b/docs/notebooks/widget_segmentations_beta.ipynb new file mode 100644 index 0000000..6c82c42 --- /dev/null +++ b/docs/notebooks/widget_segmentations_beta.ipynb @@ -0,0 +1,104 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "nbsphinx": "hidden" + }, + "source": [ + "# Vitessce Widget Tutorial" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from vitessce import (\n", + " VitessceConfig,\n", + " Component as cm,\n", + " CoordinationType as ct,\n", + " OmeTiffWrapper,\n", + " MultiImageWrapper,\n", + " CoordinationLevel as CL,\n", + " ObsSegmentationsOmeTiffWrapper,\n", + " ImageOmeTiffWrapper,\n", + " get_initial_coordination_scope_prefix,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vc = VitessceConfig(schema_version=\"1.0.16\")\n", + "dataset = vc.add_dataset(name='Spraggins').add_object(\n", + " ImageOmeTiffWrapper(\n", + " img_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2_bf.ome.tif\",\n", + " offsets_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2_bf.offsets.json\"\n", + " )\n", + ").add_object(\n", + " ObsSegmentationsOmeTiffWrapper(\n", + " img_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2.ome.tif\",\n", + " offsets_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2.offsets.json\",\n", + " obs_types_from_channel_names=True\n", + " )\n", + ")\n", + "\n", + "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n", + "lc = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n", + "\n", + "vc.link_views_by_dict([spatial, lc], {\n", + " \"imageLayer\": CL([\n", + " {\n", + " \"photometricInterpretation\": \"RGB\" \n", + " }\n", + " ]),\n", + "}, meta=True, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n", + "\n", + "vc.layout(spatial | lc);" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vw = vc.widget()\n", + "vw" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "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": "3.9.0" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +}