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Plugin class (#350)
* WIP: class to encapsulate widget logic * Potentially working widget things * Example of chat plugin * Lint * Update * Update
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8 files changed

+454
-34
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‎.coveragerc_omit‎

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@@ -10,4 +10,5 @@ omit =
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vitessce/data_utils/anndata.py
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vitessce/data_utils/ome.py
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vitessce/data_utils/entities.py
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vitessce/data_utils/multivec.py
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vitessce/data_utils/multivec.py
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vitessce/widget_plugins/demo_plugin.py

‎docs/notebooks/widget_plugin_custom.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {
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"nbsphinx": "hidden"
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},
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"source": [
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 18,
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"metadata": {},
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"outputs": [],
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"source": [
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"from vitessce import (\n",
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" VitessceConfig,\n",
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" Component as cm,\n",
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" CoordinationType as ct,\n",
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" OmeTiffWrapper,\n",
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" MultiImageWrapper,\n",
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" VitesscePlugin\n",
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")\n",
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"from esbuild_py import transform"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 40,
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"metadata": {},
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"outputs": [],
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"source": [
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"PLUGIN_ESM = transform(\"\"\"\n",
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"function createPlugins(utilsForPlugins) {\n",
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" const {\n",
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" React,\n",
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" PluginFileType,\n",
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" PluginViewType,\n",
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" PluginCoordinationType,\n",
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" PluginJointFileType,\n",
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" z,\n",
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" useCoordination,\n",
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" invokeCommand,\n",
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" } = utilsForPlugins;\n",
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" \n",
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" const CSS = `\n",
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" .chat {\n",
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" overflow-y: scroll;\n",
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" }\n",
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" `;\n",
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" \n",
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" function ChatView(props) {\n",
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" \n",
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" const [nextMessage, setNextMessage] = React.useState('');\n",
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" const [isLoading, setIsLoading] = React.useState(false);\n",
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" const [chatHistory, setChatHistory] = React.useState([]); // chatHistory is an array of message objects like [{ user, text }, ...]\n",
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" \n",
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" async function handleClick() { \n",
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" setChatHistory(prev => ([\n",
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" ...prev,\n",
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" { user: 'You', text: nextMessage },\n",
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" ]));\n",
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" setIsLoading(true);\n",
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" const [chatReceiveValue, chatReceiveBuffers] = await invokeCommand(\"chat_send\", nextMessage, []);\n",
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" setChatHistory(prev => ([\n",
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" ...prev,\n",
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" { user: 'AI', text: chatReceiveValue.text },\n",
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" ]));\n",
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" setIsLoading(false);\n",
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" }\n",
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" \n",
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" return (\n",
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" <>\n",
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" <style>{CSS}</style>\n",
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" <div className=\"chat\">\n",
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" <p>Chat view</p>\n",
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" <div>\n",
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" {chatHistory.map(message => (\n",
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" <p key={`${message.user}-${message.text}`}>\n",
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" <b>{message.user}</b>:\n",
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" <span>{message.text}</span>\n",
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" </p>\n",
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" ))}\n",
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" </div>\n",
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" <input type=\"text\" value={nextMessage} onChange={e => setNextMessage(e.target.value)} disabled={isLoading} />\n",
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" <button onClick={handleClick}>Send message</button>\n",
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" </div>\n",
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" </>\n",
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" );\n",
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" }\n",
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"\n",
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" const pluginViewTypes = [\n",
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" new PluginViewType('chat', ChatView, []),\n",
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" ];\n",
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" return { pluginViewTypes };\n",
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"}\n",
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"export default { createPlugins };\n",
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"\"\"\")\n",
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"\n",
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"\n",
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"def handle_chat_message(message, buffers):\n",
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" return { \"text\": message.upper() }, []\n",
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"\n",
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"\n",
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"class ChatPlugin(VitesscePlugin):\n",
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" plugin_esm = PLUGIN_ESM\n",
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" commands = {\n",
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" \"chat_send\": handle_chat_message,\n",
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" }"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 41,
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"metadata": {},
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"outputs": [],
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"source": [
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"vc = VitessceConfig(schema_version=\"1.0.15\", name='Spraggins Multi-Modal', description='PAS + IMS + AF From https://portal.hubmapconsortium.org/browse/collection/6a6efd0c1a2681dc7d2faab8e4ab0bca')\n",
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"dataset = vc.add_dataset(name='Spraggins').add_object(\n",
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" MultiImageWrapper(\n",
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" image_wrappers=[\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/f4188a148e4c759092d19369d310883b/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-PAS_images/VAN0006-LK-2-85-PAS_registered.ome.tif?token=', name='PAS'),\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/2130d5f91ce61d7157a42c0497b06de8/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-AF_preIMS_images/VAN0006-LK-2-85-AF_preIMS_registered.ome.tif?token=', name='AF'),\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/be503a021ed910c0918842e318e6efa2/ometiff-pyramids/ometiffs/VAN0006-LK-2-85-IMS_PosMode_multilayer.ome.tif?token=', name='IMS Pos Mode'),\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/ca886a630b2038997a4cfbbf4abfd283/ometiff-pyramids/ometiffs/VAN0006-LK-2-85-IMS_NegMode_multilayer.ome.tif?token=', name='IMS Neg Mode')\n",
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" ],\n",
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" use_physical_size_scaling=True,\n",
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" )\n",
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")\n",
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"spatial = vc.add_view(cm.SPATIAL, dataset=dataset)\n",
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"status = vc.add_view(\"chat\", dataset=dataset)\n",
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"lc = vc.add_view(cm.LAYER_CONTROLLER, dataset=dataset).set_props(disableChannelsIfRgbDetected=True)\n",
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"vc.layout(spatial | (lc / status));"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## 2. Create the Vitessce widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 42,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "52bbdb1e3f91423b8dd934e3a4ff796e",
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"version_major": 2,
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"version_minor": 1
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},
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"text/plain": [
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"VitessceWidget(config={'version': '1.0.15', 'name': 'Spraggins Multi-Modal', 'description': 'PAS + IMS + AF Fr…"
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]
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},
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"execution_count": 42,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"vw = vc.widget(plugins=[ChatPlugin()])\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.0"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎docs/notebooks/widget_plugin_demo.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {
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"nbsphinx": "hidden"
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},
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"source": [
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of Multi-Modal Imaging Data\n",
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"We visualize IMS, PAS, and AF imaging data overlaid from the Spraggins Lab of the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University, uploaded to the HuBMAP data portal."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"from vitessce import (\n",
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" VitessceConfig,\n",
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" Component as cm,\n",
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" CoordinationType as ct,\n",
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" OmeTiffWrapper,\n",
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" MultiImageWrapper,\n",
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")\n",
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"from os.path import join"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"from vitessce.widget_plugins import DemoPlugin"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## 1. Configure Vitessce\n",
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"Set up the images from the three different assays, with the `use_physical_size_scaling` set to `True` so that the IMS image scales to the other images based on their physical sizes."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"vc = VitessceConfig(schema_version=\"1.0.15\", name='Spraggins Multi-Modal', description='PAS + IMS + AF From https://portal.hubmapconsortium.org/browse/collection/6a6efd0c1a2681dc7d2faab8e4ab0bca')\n",
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"dataset = vc.add_dataset(name='Spraggins').add_object(\n",
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" MultiImageWrapper(\n",
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" image_wrappers=[\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/f4188a148e4c759092d19369d310883b/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-PAS_images/VAN0006-LK-2-85-PAS_registered.ome.tif?token=', name='PAS'),\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/2130d5f91ce61d7157a42c0497b06de8/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-AF_preIMS_images/VAN0006-LK-2-85-AF_preIMS_registered.ome.tif?token=', name='AF'),\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/be503a021ed910c0918842e318e6efa2/ometiff-pyramids/ometiffs/VAN0006-LK-2-85-IMS_PosMode_multilayer.ome.tif?token=', name='IMS Pos Mode'),\n",
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" OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/ca886a630b2038997a4cfbbf4abfd283/ometiff-pyramids/ometiffs/VAN0006-LK-2-85-IMS_NegMode_multilayer.ome.tif?token=', name='IMS Neg Mode')\n",
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" ],\n",
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" use_physical_size_scaling=True,\n",
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" )\n",
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")\n",
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"spatial = vc.add_view(cm.SPATIAL, dataset=dataset)\n",
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"status = vc.add_view(\"demo\", dataset=dataset)\n",
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"lc = vc.add_view(cm.LAYER_CONTROLLER, dataset=dataset).set_props(disableChannelsIfRgbDetected=True)\n",
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"vc.layout(spatial | (lc / status));"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## 2. Create the Vitessce widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "837fec6d047c4f83be8530996e324fb9",
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"version_major": 2,
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"version_minor": 1
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},
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"text/plain": [
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"VitessceWidget(config={'version': '1.0.15', 'name': 'Spraggins Multi-Modal', 'description': 'PAS + IMS + AF Fr…"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"vw = vc.widget(plugins=[DemoPlugin()])\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.0"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎pyproject.toml‎

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@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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[project]
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name = "vitessce"
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version = "3.2.8"
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version = "3.3.0"
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authors = [
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{ name="Mark Keller", email="[email protected]" },
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]
@@ -19,10 +19,11 @@ classifiers = [
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'Intended Audience :: Developers',
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'Intended Audience :: Science/Research',
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'Topic :: Multimedia :: Graphics',
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'Programming Language :: Python :: 3.7',
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'Programming Language :: Python :: 3.8',
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'Programming Language :: Python :: 3.9',
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'Programming Language :: Python :: 3.10',
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'Programming Language :: Python :: 3.11',
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'Programming Language :: Python :: 3.12',
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]
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dependencies = [
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'zarr>=2.5.0',

‎vitessce/__init__.py‎

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# We allow installation without all of the dependencies that the widget requires.
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# The imports below will fail in that case, and corresponding globals will be undefined.
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try:
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from .widget import VitessceWidget, data_server
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from .widget import VitessceWidget, VitesscePlugin, data_server
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except ModuleNotFoundError as e: # pragma: no cover
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warn(f'Extra installs are necessary to use widgets: {e}')
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