From 0efee88adf5469425c123e8cba73ce7387a115df Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Mon, 27 Jul 2026 20:00:11 -0400 Subject: [PATCH 1/8] Wrapper classee added for segmentation and annotations --- src/vitessce/wrappers.py | 106 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 105 insertions(+), 1 deletion(-) diff --git a/src/vitessce/wrappers.py b/src/vitessce/wrappers.py index 82e0b14e..f6f47c25 100644 --- a/src/vitessce/wrappers.py +++ b/src/vitessce/wrappers.py @@ -4,7 +4,7 @@ from collections import defaultdict import os -from os.path import join +from os.path import join, isdir import tempfile from typing import Callable, Optional, Type, TypeVar, Union from uuid import uuid4 @@ -1642,3 +1642,107 @@ def genomic_profiles_file_def_creator(base_url): obj_file_def['requestInit'] = self._request_init return obj_file_def return genomic_profiles_file_def_creator + +class ObsSegmentationsNgPrecomputedWrapper(AbstractWrapper): + """ + Wrap a Neuroglancer precomputed segmentation + meshes directory + (as produced by e.g. tissue_map_tools's igneous_converters functions). + """ + def __init__(self, data_path=None, data_url=None, coordination_values=None, options=None, **kwargs): + super().__init__(**kwargs) + raise_error_if_zero_or_more_than_one([data_path, data_url]) + self._data_path = data_path + self._data_url = data_url + self._coordination_values = coordination_values + self._options = options + self.is_remote = data_url is not None + self.local_dir_uid = "ng_precomputed_segmentation" + self._repr = make_repr(locals()) + + def convert_and_save(self, dataset_uid, obj_i, base_dir=None): + super().convert_and_save(dataset_uid, obj_i, base_dir=base_dir) + self.file_def_creators.append(self.make_file_def_creator(dataset_uid, obj_i)) + self.routes += self.make_routes(dataset_uid, obj_i) + + def make_routes(self, dataset_uid, obj_i): + if not self.is_remote: + if not isdir(self._data_path): + raise ValueError(f"data_path {self._data_path} is not a directory") + return self.get_local_dir_route(dataset_uid, obj_i, self._data_path, self.local_dir_uid) + return [] + + def get_data_url(self, base_url="", dataset_uid="", obj_i=""): + if self.is_remote: + return self._data_url + return self.get_local_dir_url(base_url, dataset_uid, obj_i, self._data_path, self.local_dir_uid) + + def make_file_def_creator(self, dataset_uid, obj_i): + def file_def_creator(base_url): + file_def = { + "fileType": "obsSegmentations.ng-precomputed", + "url": self.get_data_url(base_url, dataset_uid, obj_i), + } + if self._coordination_values is not None: + file_def["coordinationValues"] = self._coordination_values + if self._options is not None: + file_def["options"] = self._options + return file_def + return file_def_creator + +class ObsPointsNgAnnotationsWrapper(AbstractWrapper): + """ + Wrap a single Neuroglancer precomputed point-annotation directory + (e.g. one produced by tissue_map_tools's + from_spatialdata_points_to_precomputed_points). + + :param str data_path: Path to a local annotation directory (a subdirectory + of a precomputed root, containing its own `info` file). Mutually + exclusive with `data_url`. + :param str data_url: URL to a remote annotation directory already being + served. Mutually exclusive with `data_path`. + :param dict coordination_values: Coordination values for this file, e.g. + `{"fileUid": "annotation_inv_points"}`. + :param dict options: Options for this file type, e.g. + `{"featureIndexProp": "phenotype", "pointIndexProp": "cell_id"}`. + """ + + def __init__(self, data_path=None, data_url=None, coordination_values=None, options=None, **kwargs): + super().__init__(**kwargs) + raise_error_if_zero_or_more_than_one([data_path, data_url]) + self._data_path = data_path + self._data_url = data_url + self._coordination_values = coordination_values + self._options = options + self.is_remote = data_url is not None + self.local_dir_uid = "ng_precomputed_annotations" + self._repr = make_repr(locals()) + + def convert_and_save(self, dataset_uid, obj_i, base_dir=None): + super().convert_and_save(dataset_uid, obj_i, base_dir=base_dir) + self.file_def_creators.append(self.make_file_def_creator(dataset_uid, obj_i)) + self.routes += self.make_routes(dataset_uid, obj_i) + + def make_routes(self, dataset_uid, obj_i): + if not self.is_remote: + if not isdir(self._data_path): + raise ValueError(f"data_path {self._data_path} is not a directory") + return self.get_local_dir_route(dataset_uid, obj_i, self._data_path, self.local_dir_uid) + return [] + + def get_data_url(self, base_url="", dataset_uid="", obj_i=""): + if self.is_remote: + return self._data_url + return self.get_local_dir_url(base_url, dataset_uid, obj_i, self._data_path, self.local_dir_uid) + + def make_file_def_creator(self, dataset_uid, obj_i): + def file_def_creator(base_url): + file_def = { + "fileType": "obsPoints.ng-annotations", + "url": self.get_data_url(base_url, dataset_uid, obj_i), + } + if self._coordination_values is not None: + file_def["coordinationValues"] = self._coordination_values + if self._options is not None: + file_def["options"] = self._options + return file_def + return file_def_creator From 015c05a9f5592d4ed89d3205e5e5ef79811c9495 Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Tue, 28 Jul 2026 08:36:58 -0400 Subject: [PATCH 2/8] Example notebook added --- .../widget_neuroglancer_precomputed.ipynb | 179 ++++++++++++++++++ 1 file changed, 179 insertions(+) create mode 100644 docs/notebooks/widget_neuroglancer_precomputed.ipynb diff --git a/docs/notebooks/widget_neuroglancer_precomputed.ipynb b/docs/notebooks/widget_neuroglancer_precomputed.ipynb new file mode 100644 index 00000000..be1844f7 --- /dev/null +++ b/docs/notebooks/widget_neuroglancer_precomputed.ipynb @@ -0,0 +1,179 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "08d489b0", + "metadata": {}, + "source": [ + "# Vitessce Widget Tutorial" + ] + }, + { + "cell_type": "markdown", + "id": "d6dda7d0", + "metadata": {}, + "source": [ + "# Example usage of Neuroglancer precomputed segmentations and annotations\n", + "\n", + "This notebook demonstrates `ObsSegmentationsNgPrecomputedWrapper` and `ObsPointsNgAnnotationsWrapper`, which wrap Neuroglancer precomputed segmentation/mesh data and point-annotation data (e.g. as produced by the [tissue-map-tools](https://github.com/hms-dbmi/tissue-map-tools) library) for use with the `neuroglancer` and `layerControllerBeta` views.\n", + "\n", + "The `obsSets`-type file (and its corresponding view) is required for the segmentation layer to actually resolve and display any segments -- without it, segments will not be selected/colored dynamically. A static `segments` list can alternatively be passed via `options` for quick testing without a full `obsSets` pipeline." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6d673a85", + "metadata": {}, + "outputs": [], + "source": [ + "from vitessce import (\n", + " VitessceConfig,\n", + " CoordinationLevel as CL,\n", + " get_initial_coordination_scope_prefix,\n", + " ObsSegmentationsNgPrecomputedWrapper,\n", + " CsvWrapper,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "8c5bcdc5", + "metadata": {}, + "source": [ + "## 1. Configure Vitessce" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ac0fb259", + "metadata": {}, + "outputs": [], + "source": [ + "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Neuroglancer precomputed example\")\n", + "dataset = vc.add_dataset(\"Melanoma\")\n", + "\n", + "# A Neuroglancer precomputed segmentation meshes directory.\n", + "# fileUid here must match the value used below in link_views_by_dict's\n", + "# segmentationLayer coordination.\n", + "dataset.add_object(ObsSegmentationsNgPrecomputedWrapper(\n", + " data_url=\"https://data-2.vitessce.io/data/sorger/melanoma_meshes\",\n", + " coordination_values={\"fileUid\": \"segmentation\"},\n", + "))\n", + "\n", + "# An obsSets-type file is required for segments to be dynamically\n", + "# selected/colored -- obsType here must match the segmentationChannel's\n", + "# obsType coordination value set below.\n", + "dataset.add_object(CsvWrapper(\n", + " csv_url=\"https://storage.googleapis.com/vitessce-demo-data/neuroglancer-march-2025/melanoma_with_embedding_filtered_ids.csv\",\n", + " data_type=\"obsSets\",\n", + " coordination_values={\"obsType\": \"cell\"},\n", + " options={\n", + " \"obsIndex\": \"id\",\n", + " \"obsSets\": [{\"name\": \"Clusters\", \"column\": \"cluster\"}],\n", + " },\n", + "))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6babd185", + "metadata": {}, + "outputs": [], + "source": [ + "ng_view = vc.add_view(\"neuroglancer\", dataset=dataset)\n", + "lc_view = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n", + "# TODO: until support to load the segments is added in NG-View\n", + "# The obsSets view is not required for the segmentation to load, but\n", + "# a mounted obsSets view is needed to trigger the underlying data hook \n", + "# that resolves obsSets data for the segmentation channel.\n", + "obs_sets_view = vc.add_view(\"obsSets\", dataset=dataset)\n", + "vc.layout(ng_view | lc_view | obs_sets_view)" + ] + }, + { + "cell_type": "markdown", + "id": "c8aaa012", + "metadata": {}, + "source": [ + "## 2. Coordinate the views\n", + "\n", + "Two separate `link_views_by_dict` calls are needed:\n", + "- A plain (non-meta) link for shared spatial rendering mode and camera position/rotation.\n", + "- A multi-level (meta) link for the segmentation layer + channel, mirroring the shape\n", + " `obsSegmentations.ng-precomputed` files require to resolve correctly." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "648ca751", + "metadata": {}, + "outputs": [], + "source": [ + "vc.link_views_by_dict([ng_view, lc_view], {\n", + " \"spatialRenderingMode\": \"3D\",\n", + " \"spatialZoom\": 0,\n", + " \"spatialTargetX\": 0,\n", + " \"spatialTargetY\": 0,\n", + " \"spatialTargetZ\": 0,\n", + " \"spatialRotationX\": 0,\n", + " \"spatialRotationY\": 0,\n", + " \"spatialRotationOrbit\": 0,\n", + "}, meta=False)\n", + "\n", + "vc.link_views_by_dict([ng_view, lc_view], {\n", + " \"segmentationLayer\": CL([{\n", + " \"fileUid\": \"segmentation\",\n", + " \"spatialLayerOpacity\": 1,\n", + " \"spatialTargetResolution\": None,\n", + " \"spatialLayerVisible\": True,\n", + " \"segmentationChannel\": CL([{\"obsType\": \"cell\", \"spatialChannelVisible\": True}]),\n", + " }]),\n", + "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))" + ] + }, + { + "cell_type": "markdown", + "id": "10210740", + "metadata": {}, + "source": [ + "## 3. Create the Vitessce widget" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f562bfc8", + "metadata": {}, + "outputs": [], + "source": [ + "vw = vc.widget()\n", + "vw" + ] + } + ], + "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": "3.10.14" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From a0151619555b4e32bde4042323b34be5bcc8ec74 Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Tue, 28 Jul 2026 08:40:14 -0400 Subject: [PATCH 3/8] Exports added --- src/vitessce/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/vitessce/__init__.py b/src/vitessce/__init__.py index d60c306c..fcf60036 100644 --- a/src/vitessce/__init__.py +++ b/src/vitessce/__init__.py @@ -50,6 +50,8 @@ ImageOmeZarrWrapper, ObsSegmentationsOmeZarrWrapper, SpatialDataWrapper, + ObsSegmentationsNgPrecomputedWrapper, + ObsPointsNgAnnotationsWrapper, ) except ModuleNotFoundError as e: # pragma: no cover warn(f'Extra installs are necessary to use wrappers: {e}') From b85890854e633954b11752af9e5f9a9ad1231d9e Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Tue, 28 Jul 2026 10:40:47 -0400 Subject: [PATCH 4/8] Lint and tests --- src/vitessce/wrappers.py | 2 + tests/test_wrappers.py | 70 ++ uv.lock | 1553 ++++++++++++-------------------------- 3 files changed, 567 insertions(+), 1058 deletions(-) diff --git a/src/vitessce/wrappers.py b/src/vitessce/wrappers.py index f6f47c25..9fc871d4 100644 --- a/src/vitessce/wrappers.py +++ b/src/vitessce/wrappers.py @@ -1643,6 +1643,7 @@ def genomic_profiles_file_def_creator(base_url): return obj_file_def return genomic_profiles_file_def_creator + class ObsSegmentationsNgPrecomputedWrapper(AbstractWrapper): """ Wrap a Neuroglancer precomputed segmentation + meshes directory @@ -1689,6 +1690,7 @@ def file_def_creator(base_url): return file_def return file_def_creator + class ObsPointsNgAnnotationsWrapper(AbstractWrapper): """ Wrap a single Neuroglancer precomputed point-annotation directory diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py index 046108f1..0a7e7efd 100644 --- a/tests/test_wrappers.py +++ b/tests/test_wrappers.py @@ -21,6 +21,8 @@ ObsSegmentationsOmeTiffWrapper, ImageOmeZarrWrapper, ObsSegmentationsOmeZarrWrapper, + ObsSegmentationsNgPrecomputedWrapper, + ObsPointsNgAnnotationsWrapper, ) from vitessce.wrappers import SpatialDataWrapper, file_path_to_url_path @@ -529,3 +531,71 @@ def test_spatial_data_with_base_dir_2(self): "obsType": "spot" } }) + def test_obs_segmentations_ng_precomputed_local(self): + w = ObsSegmentationsNgPrecomputedWrapper( + data_path=data_path / 'test.ng.precomputed', + coordination_values={'fileUid': 'segmentation'}, + options={'segments': ['1', '2', '3']}, + ) + w.local_dir_uid = 'test.ng.precomputed' + + file_def_creator = w.make_file_def_creator("A", "0") + file_def = file_def_creator('http://localhost:8000') + self.assertEqual(file_def, { + 'fileType': 'obsSegmentations.ng-precomputed', + 'url': 'http://localhost:8000/A/0/test.ng.precomputed', + 'coordinationValues': {'fileUid': 'segmentation'}, + 'options': {'segments': ['1', '2', '3']}, + }) + + def test_obs_segmentations_ng_precomputed_remote(self): + w = ObsSegmentationsNgPrecomputedWrapper( + data_url='https://example.com/data/precomputed', + coordination_values={'fileUid': 'segmentation'}, + ) + file_def_creator = w.make_file_def_creator("A", "0") + file_def = file_def_creator('http://localhost:8000') + self.assertEqual(file_def, { + 'fileType': 'obsSegmentations.ng-precomputed', + 'url': 'https://example.com/data/precomputed', + 'coordinationValues': {'fileUid': 'segmentation'}, + }) + self.assertEqual(w.make_routes("A", "0"), []) + + def test_obs_segmentations_ng_precomputed_requires_exactly_one_source(self): + with self.assertRaises(ValueError): + ObsSegmentationsNgPrecomputedWrapper() + with self.assertRaises(ValueError): + ObsSegmentationsNgPrecomputedWrapper( + data_path=data_path / 'test.ng.precomputed', + data_url='https://example.com/data/precomputed', + ) + + def test_obs_points_ng_annotations_local(self): + w = ObsPointsNgAnnotationsWrapper( + data_path=data_path / 'test.ng.annotations', + coordination_values={'fileUid': 'annotation_points'}, + options={'featureIndexProp': 'phenotype', 'pointIndexProp': 'cell_id'}, + ) + w.local_dir_uid = 'test.ng.annotations' + + file_def_creator = w.make_file_def_creator("A", "0") + file_def = file_def_creator('http://localhost:8000') + self.assertEqual(file_def, { + 'fileType': 'obsPoints.ng-annotations', + 'url': 'http://localhost:8000/A/0/test.ng.annotations', + 'coordinationValues': {'fileUid': 'annotation_points'}, + 'options': {'featureIndexProp': 'phenotype', 'pointIndexProp': 'cell_id'}, + }) + + def test_obs_points_ng_annotations_remote(self): + w = ObsPointsNgAnnotationsWrapper( + data_url='https://example.com/data/annotations', + ) + file_def_creator = w.make_file_def_creator("A", "0") + file_def = file_def_creator('http://localhost:8000') + self.assertEqual(file_def, { + 'fileType': 'obsPoints.ng-annotations', + 'url': 'https://example.com/data/annotations', + }) + self.assertEqual(w.make_routes("A", "0"), []) diff --git a/uv.lock b/uv.lock index 16a969ea..295512fc 100644 --- a/uv.lock +++ b/uv.lock @@ -1,9 +1,22 @@ version = 1 -requires-python = ">=3.10" -resolution-markers = [ - "python_full_version < '3.11'", - "python_full_version == '3.11.*'", - "python_full_version >= '3.12'", +requires-python = ">=3.12" + +[[package]] +name = "aiobotocore" +version = "2.23.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "aiohttp" }, + { name = "aioitertools" }, + { name = "botocore" }, + { name = "jmespath" }, 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"https://files.pythonhosted.org/packages/b7/1a/7e4798e9339adc931158c9d69ecc34f5e6791489d469f5e50ec15e35f458/zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931", size = 9630 }, -] From 82671ac0957899a7bcdab81f79bd1ac62f499f53 Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Tue, 28 Jul 2026 12:27:19 -0400 Subject: [PATCH 5/8] Added jsx-runtime to the importMaps --- src/vitessce/widget.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/vitessce/widget.py b/src/vitessce/widget.py index 583193c5..f04c2f3f 100644 --- a/src/vitessce/widget.py +++ b/src/vitessce/widget.py @@ -175,6 +175,8 @@ def get_uid_str(uid): const importMap = { imports: { "react": "https://esm.sh/react@18.2.0?dev", + // needed when using custom_js_url + "react/jsx-runtime": "https://esm.sh/react@18.2.0/jsx-runtime?dev", "react-dom": "https://esm.sh/react-dom@18.2.0?dev", "react-dom/client": "https://esm.sh/react-dom@18.2.0/client?dev", }, @@ -184,6 +186,8 @@ def get_uid_str(uid): "react": "https://cdn.vitessce.io/react@18.2.0/index.js", "react-dom": "https://cdn.vitessce.io/react-dom@18.2.0/index.js", "react-dom/client": "https://cdn.vitessce.io/react-dom@18.2.0/es2022/client.mjs", + // needed when using custom_js_url + "react/jsx-runtime": "https://esm.sh/react@18.2.0/jsx-runtime?dev", // Replaced with version-specific URL below. "vitessce": "https://cdn.vitessce.io/vitessce@VERSION/dist/index.min.js", }, From 7fab712894c331d35f3cb25c31f77ab0193a2199 Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Tue, 28 Jul 2026 12:31:32 -0400 Subject: [PATCH 6/8] Notebook layout fix --- .../widget_neuroglancer_precomputed.ipynb | 396 +++++++++++++++++- 1 file changed, 379 insertions(+), 17 deletions(-) diff --git a/docs/notebooks/widget_neuroglancer_precomputed.ipynb b/docs/notebooks/widget_neuroglancer_precomputed.ipynb index be1844f7..80aacdfd 100644 --- a/docs/notebooks/widget_neuroglancer_precomputed.ipynb +++ b/docs/notebooks/widget_neuroglancer_precomputed.ipynb @@ -22,9 +22,11 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "id": "6d673a85", - "metadata": {}, + "metadata": { + "tags": [] + }, "outputs": [], "source": [ "from vitessce import (\n", @@ -46,10 +48,23 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "id": "ac0fb259", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Neuroglancer precomputed example\")\n", "dataset = vc.add_dataset(\"Melanoma\")\n", @@ -78,10 +93,23 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "6babd185", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ng_view = vc.add_view(\"neuroglancer\", dataset=dataset)\n", "lc_view = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n", @@ -90,7 +118,7 @@ "# a mounted obsSets view is needed to trigger the underlying data hook \n", "# that resolves obsSets data for the segmentation channel.\n", "obs_sets_view = vc.add_view(\"obsSets\", dataset=dataset)\n", - "vc.layout(ng_view | lc_view | obs_sets_view)" + "vc.layout(ng_view | (lc_view / obs_sets_view))" ] }, { @@ -108,10 +136,23 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "id": "648ca751", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "vc.link_views_by_dict([ng_view, lc_view], {\n", " \"spatialRenderingMode\": \"3D\",\n", @@ -145,14 +186,48 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "id": "f562bfc8", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "dbd6e9854d6442ab80ba290784996dda", + "version_major": 2, + "version_minor": 1 + }, + "text/plain": [ + "" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "vw = vc.widget()\n", + "vw = vc.widget(custom_js_url=\"http://localhost:9001/packages/main/dev/dist/index.js\")\n", "vw" ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "be0c7d7e-e466-45c2-8b65-503501d6faf9", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8fbd9181-2d33-4018-be02-722161342c5c", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -171,7 +246,294 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.14" + "version": "3.12.13" + }, + "widgets": { + "application/vnd.jupyter.widget-state+json": { + "state": { + "7944f55009c64754a407dfff3408ca92": { + "model_module": "@jupyter-widgets/base", + "model_module_version": "2.0.0", + "model_name": "LayoutModel", + "state": { + "_model_module": "@jupyter-widgets/base", + "_model_module_version": "2.0.0", + "_model_name": "LayoutModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/base", + "_view_module_version": "2.0.0", + "_view_name": "LayoutView", + "align_content": null, + "align_items": null, + "align_self": null, + "border_bottom": null, + "border_left": null, + "border_right": null, + "border_top": null, + "bottom": null, + "display": null, + "flex": null, + "flex_flow": null, + "grid_area": null, + "grid_auto_columns": null, + "grid_auto_flow": null, + "grid_auto_rows": null, + "grid_column": null, + "grid_gap": null, + "grid_row": null, + "grid_template_areas": null, + "grid_template_columns": null, + "grid_template_rows": null, + "height": null, + "justify_content": null, + "justify_items": null, + "left": null, + "margin": null, + "max_height": null, + "max_width": null, + "min_height": null, + "min_width": null, + "object_fit": null, + "object_position": null, + "order": null, + "overflow": null, + "padding": null, + "right": null, + "top": null, + "visibility": null, + "width": null + } + }, + "c9218e280b5e411aacd04560cbb1ea89": { + "model_module": "anywidget", + "model_module_version": "~0.11.*", + "model_name": "AnyModel", + "state": { + "_anywidget_id": "vitessce.widget.VitessceWidget", + "_config": { + "coordinationSpace": { + "dataset": { + "A": "A" + }, + "fileUid": { + "init_A_obsSegmentations_0": "segmentation" + }, + "metaCoordinationScopes": { + "init_A_obsSegmentations_0": { + "segmentationLayer": [ + "init_A_obsSegmentations_0" + ] + } + }, + "metaCoordinationScopesBy": { + "init_A_obsSegmentations_0": { + "segmentationChannel": { + "obsType": { + "init_A_obsSegmentations_0": "init_A_obsSegmentations_0" + }, + "spatialChannelVisible": { + "init_A_obsSegmentations_0": "init_A_obsSegmentations_0" + } + }, + "segmentationLayer": { + "fileUid": { + "init_A_obsSegmentations_0": "init_A_obsSegmentations_0" + }, + "segmentationChannel": { + "init_A_obsSegmentations_0": [ + "init_A_obsSegmentations_0" + ] + }, + "spatialLayerOpacity": { + "init_A_obsSegmentations_0": "init_A_obsSegmentations_0" + }, + "spatialLayerVisible": { + "init_A_obsSegmentations_0": "init_A_obsSegmentations_0" + }, + "spatialTargetResolution": { + "init_A_obsSegmentations_0": "init_A_obsSegmentations_0" + } + } + } + }, + "obsType": { + "init_A_obsSegmentations_0": "cell" + }, + "segmentationChannel": { + "init_A_obsSegmentations_0": "__dummy__" + }, + "segmentationLayer": { + "init_A_obsSegmentations_0": "__dummy__" + }, + "spatialChannelVisible": { + "init_A_obsSegmentations_0": true + }, + "spatialLayerOpacity": { + "init_A_obsSegmentations_0": 1 + }, + "spatialLayerVisible": { + "init_A_obsSegmentations_0": true + }, + "spatialRenderingMode": { + "A": "3D" + }, + "spatialRotationOrbit": { + "A": 0 + }, + "spatialRotationX": { + "A": 0 + }, + "spatialRotationY": { + "A": 0 + }, + "spatialTargetResolution": { + "init_A_obsSegmentations_0": null + }, + "spatialTargetX": { + "A": 0 + }, + "spatialTargetY": { + "A": 0 + }, + "spatialTargetZ": { + "A": 0 + }, + "spatialZoom": { + "A": 0 + } + }, + "datasets": [ + { + "files": [ + { + "coordinationValues": { + "fileUid": "segmentation" + }, + "fileType": "obsSegmentations.ng-precomputed", + "url": "https://data-2.vitessce.io/data/sorger/melanoma_meshes" + }, + { + "coordinationValues": { + "obsType": "cell" + }, + "fileType": "obsSets.csv", + "options": { + "obsIndex": "id", + "obsSets": [ + { + "column": "cluster", + "name": "Clusters" + } + ] + }, + "url": "https://storage.googleapis.com/vitessce-demo-data/neuroglancer-march-2025/melanoma_with_embedding_filtered_ids.csv" + } + ], + "name": "Melanoma", + "uid": "A" + } + ], + "description": "", + "initStrategy": "auto", + "layout": [ + { + "component": "neuroglancer", + "coordinationScopes": { + "dataset": "A", + "metaCoordinationScopes": [ + "init_A_obsSegmentations_0" + ], + "metaCoordinationScopesBy": [ + "init_A_obsSegmentations_0" + ], + "spatialRenderingMode": "A", + "spatialRotationOrbit": "A", + "spatialRotationX": "A", + "spatialRotationY": "A", + "spatialTargetX": "A", + "spatialTargetY": "A", + "spatialTargetZ": "A", + "spatialZoom": "A" + }, + "coordinationScopesBy": {}, + "h": 12, + "w": 3, + "x": 0, + "y": 0 + }, + { + "component": "layerControllerBeta", + "coordinationScopes": { + "dataset": "A", + "metaCoordinationScopes": [ + "init_A_obsSegmentations_0" + ], + "metaCoordinationScopesBy": [ + "init_A_obsSegmentations_0" + ], + "spatialRenderingMode": "A", + "spatialRotationOrbit": "A", + "spatialRotationX": "A", + "spatialRotationY": "A", + "spatialTargetX": "A", + "spatialTargetY": "A", + "spatialTargetZ": "A", + "spatialZoom": "A" + }, + "coordinationScopesBy": {}, + "h": 12, + "w": 3, + "x": 3, + "y": 0 + }, + { + "component": "obsSets", + "coordinationScopes": { + "dataset": "A" + }, + "h": 12, + "w": 6, + "x": 6, + "y": 0 + } + ], + "name": "Neuroglancer precomputed example", + "version": "1.0.17" + }, + "_dom_classes": [], + "_esm": "\nlet importWithMap;\ntry {\n importWithMap = (await import('https://unpkg.com/dynamic-importmap@0.1.0')).importWithMap;\n} catch(e) {\n console.warn(\"Import of dynamic-importmap failed, trying fallback.\");\n importWithMap = (await import('https://cdn.vitessce.io/dynamic-importmap@0.1.0/dist/index.js')).importWithMap;\n}\n\nconst successfulImportMap = {\n imports: {\n\n },\n};\nconst importMap = {\n imports: {\n \"react\": \"https://esm.sh/react@18.2.0?dev\",\n \"react-dom\": \"https://esm.sh/react-dom@18.2.0?dev\",\n \"react-dom/client\": \"https://esm.sh/react-dom@18.2.0/client?dev\",\n },\n};\nconst fallbackImportMap = {\n imports: {\n \"react\": \"https://cdn.vitessce.io/react@18.2.0/index.js\",\n \"react-dom\": \"https://cdn.vitessce.io/react-dom@18.2.0/index.js\",\n \"react-dom/client\": \"https://cdn.vitessce.io/react-dom@18.2.0/es2022/client.mjs\",\n // Replaced with version-specific URL below.\n \"vitessce\": \"https://cdn.vitessce.io/vitessce@VERSION/dist/index.min.js\",\n 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dark)').matches;\n// The jupyter server may be running through a proxy,\n// which means that the client needs to prepend the part of the URL before /proxy/8000 such as\n// https://hub.gke2.mybinder.org/user/vitessce-vitessce-python-swi31vcv/proxy/8000/A/0/cells\n// For workspaces: https://workspaces-pt.hubmapconsortium.org/passthrough/HOSTNAME/PORT/ADDITIONAL_PATH_INFO?QUERY_PARAMS=HELLO_WORLD\nfunction prependBaseUrl(config, proxy, hasHostName) {\n if (!proxy || hasHostName) {\n return config;\n }\n const { origin, pathname } = new URL(window.location.href);\n const isInWorkspaces = origin.startsWith(WORKSPACES_URL_KEYWORD);\n const jupyterLabConfigEl = document.getElementById('jupyter-config-data');\n\n let baseUrl;\n if (isInWorkspaces) {\n const pathSegments = pathname.split('/');\n const passthroughIndex = pathSegments.indexOf('passthrough');\n if (passthroughIndex !== -1) {\n baseUrl = pathSegments.slice(0, passthroughIndex + 3).join('/');\n baseUrl += '/';\n }\n } else if 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