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‎notebooks/01-Single-Spatial-View.ipynb‎

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@@ -94,7 +94,7 @@
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},
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"outputs": [],
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"source": [
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"!pip install \"vitessce[all]==3.9.2\""
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"!pip install \"vitessce[all]==3.9.2\" \"scanpy\" \"easy-vitessce==0.0.12\" \"spatialdata==0.7.3\" \"spatialdata-plot==0.4.0\""
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]
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},
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{
@@ -397,22 +397,6 @@
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"The cell below downloads a small Visium breast-cancer dataset as a `.zarr` zip archive and unzips it locally. The download only runs once — subsequent runs detect the existing directory and skip the download."
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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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"id": "ed553633-dae2-484f-b305-f7b944163c48",
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"metadata": {
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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "WkxtEEfDiLxs",
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"outputId": "2b59060d-5fa6-423c-e797-3ddcd4be6cec"
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},
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"outputs": [],
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"source": [
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"!pip install \"spatialdata==0.7.3\""
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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,
@@ -605,22 +589,6 @@
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"Because Vitessce can display multiple images at a time (i.e., multiple image _layers_), the visualization properties for imaging data are represented using a hierarchical data structure."
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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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"id": "3cc34dc2-f3ca-435c-8ad5-8ac7f33f55b7",
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"metadata": {},
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"outputs": [],
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"source": [
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"from IPython.core.display import HTML\n",
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"display(HTML(\"\"\"\n",
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"<?xml version=\"1.0\" standalone=\"no\"?>\n",
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"<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\" \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
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"<svg version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 525.5 568.5\" width=\"300px\"><!-- svg-source:excalidraw --><metadata></metadata><defs><style class=\"style-fonts\">\n",
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" @font-face { font-family: Excalifont; src: 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621-
"\"\"\"))"
622-
]
623-
},
624592
{
625593
"cell_type": "markdown",
626594
"id": "910a3a43-b2a9-4420-8ba7-13f59c19b1ef",
@@ -963,22 +931,6 @@
963931
"This means existing SpatialData-Plot workflows become interactive with just one extra import."
964932
]
965933
},
966-
{
967-
"cell_type": "code",
968-
"execution_count": null,
969-
"id": "1ea722d3-93f3-4c1b-8e24-9f7c43d1c821",
970-
"metadata": {
971-
"colab": {
972-
"base_uri": "https://localhost:8080/"
973-
},
974-
"id": "eAbhYE0pfsLw",
975-
"outputId": "2966b17a-a7ef-4a30-f7d7-b932aeb9b068"
976-
},
977-
"outputs": [],
978-
"source": [
979-
"!pip install \"spatialdata-plot==0.4.0\" \"easy_vitessce==0.0.12\""
980-
]
981-
},
982934
{
983935
"cell_type": "code",
984936
"execution_count": null,

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