usage.ipynb

{
	"cells": [
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"## Usage\n",
				"This notebook shows how to use the different widgets provided by the hra_jupyter_widgets package."
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"### Install package"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"%pip install hra_jupyter_widgets ipywidgets"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"### Import widgets"
			]
		},
		{
			"cell_type": "code",
			"execution_count": 2,
			"metadata": {},
			"outputs": [],
			"source": [
				"import ipywidgets as widgets\n",
				"from hra_jupyter_widgets import (\n",
				"    BodyUi,               # CCF 3D Body UI\n",
				"    CdeVisualization,     # Cell Distance Explorer (CDE)\n",
				"    Eui,                  # Exploration User Interface (EUI)\n",
				"    EuiOrganInformation,  # Organ Information\n",
				"    FtuExplorer,          # Functional Tissue Unit (FTU) Explorer\n",
				"    FtuExplorerSmall,     # FTU Explorer (small version)\n",
				"    MedicalIllustration,  # Medical Illustration Viewer (2D FTU Viewer)\n",
				"    ModelViewer,          # GLB model viewer\n",
				"    NodeDistVis,          # VCCF 3D Node Distance Visualization\n",
				"    Rui,                  # Registration User Interface (RUI)\n",
				")"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"### Configure organ and illustration"
			]
		},
		{
			"cell_type": "code",
			"execution_count": 3,
			"metadata": {},
			"outputs": [],
			"source": [
				"# Kidney uberon id\n",
				"organ = \"http://purl.obolibrary.org/obo/UBERON_0002113\"\n",
				"illustration = \"https://purl.humanatlas.io/2d-ftu/kidney-renal-corpuscle\""
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"### Create and use a widget"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"medical_illustration = MedicalIllustration(selected_illustration=illustration)\n",
				"display(medical_illustration)"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"# Create an output widget\n",
				"output = widgets.Output()\n",
				"\n",
				"\n",
				"# Create an event listener that prints to the output widget\n",
				"# It takes a single argument - the event data\n",
				"def cell_click(cell):\n",
				"    with output:\n",
				"        print(f\"Cell clicked: '{cell['label']}'\")\n",
				"\n",
				"\n",
				"# Register the listener\n",
				"medical_illustration.on_cell_click(cell_click)\n",
				"# Listeners can be removed by calling on_cell_click with remove=True, i.e.\n",
				"# medical_illustration.on_cell_click(cell_click, remove=True)\n",
				"\n",
				"display(output)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"### Widget showcase"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### Eui Organ Information"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"organ_info = EuiOrganInformation(organ_iri=organ)\n",
				"display(organ_info)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### Eui"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"eui = Eui()\n",
				"display(eui)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### Rui"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"rui = Rui()\n",
				"display(rui)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### FTU explorer (small version)"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"ftu_explorer_small = FtuExplorerSmall(selected_illustration=illustration)\n",
				"display(ftu_explorer_small)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### FTU explorer (full version)"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"ftu_explorer = FtuExplorer()\n",
				"display(ftu_explorer)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### 3D Model Viewer"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"model_viewer = ModelViewer(url=\"https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb\")\n",
				"display(model_viewer)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### Node distance visualization"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"node_dist_vis = NodeDistVis(\n",
				"    nodes=\"https://cdn.humanatlas.io/image-store/vccf-data-cell-nodes/published/colon-cycif-sorgerlab/CRC01002-nodes.csv\",\n",
				"    node_target_key=\"Cell Type\",\n",
				"    node_target_value=\"Endothelial\",\n",
				"    edges=\"https://cdn.humanatlas.io/image-store/vccf-data-cell-nodes/published/colon-cycif-sorgerlab/CRC01002-edges.csv\",\n",
				")\n",
				"display(node_dist_vis)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### Cell Distance Explorer"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"cde = CdeVisualization(\n",
				"    nodes=\"https://cdn.humanatlas.io/image-store/vccf-data-cell-nodes/published/colon-cycif-sorgerlab/CRC01002-nodes.csv\",\n",
				"    edges=\"https://cdn.humanatlas.io/image-store/vccf-data-cell-nodes/published/colon-cycif-sorgerlab/CRC01002-edges.csv\",\n",
				")\n",
				"display(cde)"
			]
		},
		{
			"cell_type": "markdown",
			"metadata": {},
			"source": [
				"#### Body UI"
			]
		},
		{
			"cell_type": "code",
			"execution_count": null,
			"metadata": {},
			"outputs": [],
			"source": [
				"body_ui = BodyUi(scene=\"https://apps.humanatlas.io/api/v1/reference-organ-scene?organ-iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0000059&sex=male\")\n",
				"display(body_ui)"
			]
		}
	],
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