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‎pr-22/_sources/notebooks/tutorials/common_errors.ipynb‎

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"id": "38a9546a",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:40.958364Z",
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"iopub.status.busy": "2026-08-18T23:00:40.958120Z",
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"iopub.status.idle": "2026-08-18T23:00:46.730012Z",
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"shell.execute_reply": "2026-08-18T23:00:46.729444Z"
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"iopub.execute_input": "2026-08-19T03:32:58.684716Z",
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"iopub.status.idle": "2026-08-19T03:33:04.321850Z",
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"shell.execute_reply": "2026-08-19T03:33:04.321265Z"
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}
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},
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"outputs": [
@@ -75,6 +75,56 @@
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"sdata"
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]
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},
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{
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"cell_type": "markdown",
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"id": "03f14f09",
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"metadata": {},
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"source": [
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"## 0. `AttributeError: ... object has no attribute 'pl'`\n",
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"\n",
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"The `.pl` accessor is only attached when you `import spatialdata_plot`. Forget that import and every\n",
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"`sdata.pl.…` call raises `AttributeError` — the first wall most newcomers hit. The `Setup` cell above\n",
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"already does the import; the cell below runs a *fresh* interpreter without it to show the message."
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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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"id": "d550e432",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-19T03:33:04.323735Z",
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"iopub.status.busy": "2026-08-19T03:33:04.323350Z",
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"iopub.status.idle": "2026-08-19T03:33:08.844352Z",
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"shell.execute_reply": "2026-08-19T03:33:08.843536Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"AttributeError: 'SpatialData' object has no attribute 'pl'\n"
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]
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}
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],
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"source": [
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"import os\n",
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"import subprocess\n",
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"import sys\n",
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"\n",
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"# A fresh interpreter that never imports spatialdata_plot, so `.pl` is unregistered.\n",
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"# PYTHON_COLORS=0 keeps the captured traceback free of ANSI colour codes.\n",
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"snippet = \"import spatialdata as sd; sd.datasets.blobs().pl.render_shapes('blobs_circles')\"\n",
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"result = subprocess.run(\n",
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" [sys.executable, \"-c\", snippet],\n",
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" capture_output=True,\n",
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" text=True,\n",
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" env={**os.environ, \"PYTHON_COLORS\": \"0\", \"NO_COLOR\": \"1\"},\n",
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")\n",
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"print(result.stderr.strip().splitlines()[-1])"
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]
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},
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{
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"cell_type": "markdown",
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"id": "5ec56751",
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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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"execution_count": 3,
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"id": "12b055e9",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.732100Z",
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"iopub.status.busy": "2026-08-18T23:00:46.731683Z",
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"iopub.status.idle": "2026-08-18T23:00:46.734623Z",
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"shell.execute_reply": "2026-08-18T23:00:46.734105Z"
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"iopub.execute_input": "2026-08-19T03:33:08.846271Z",
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"iopub.status.busy": "2026-08-19T03:33:08.846138Z",
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"iopub.status.idle": "2026-08-19T03:33:08.849074Z",
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"shell.execute_reply": "2026-08-19T03:33:08.848642Z"
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}
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},
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"outputs": [
@@ -128,14 +178,14 @@
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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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"execution_count": 4,
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"id": "86745998",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.735964Z",
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"iopub.status.busy": "2026-08-18T23:00:46.735841Z",
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"iopub.status.idle": "2026-08-18T23:00:46.738032Z",
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"shell.execute_reply": "2026-08-18T23:00:46.737590Z"
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"iopub.execute_input": "2026-08-19T03:33:08.850507Z",
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"iopub.status.busy": "2026-08-19T03:33:08.850389Z",
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"iopub.status.idle": "2026-08-19T03:33:08.852860Z",
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"shell.execute_reply": "2026-08-19T03:33:08.852432Z"
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}
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},
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"outputs": [
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" print(\"KeyError:\", e)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "9c53205c",
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"metadata": {},
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"source": [
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"## 3. Ambiguous colour/column name\n",
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"\n",
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"If a `color` string is **both** a valid matplotlib colour name and a column in the element or its\n",
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"annotating table, `spatialdata-plot` cannot tell which you meant and raises. Disambiguate with a hex\n",
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"string or an RGB(A) tuple, or rename the column. Here we deliberately add a column called `red` to\n",
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"force the clash."
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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": 5,
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"id": "dac9e6a7",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-19T03:33:08.854274Z",
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"iopub.status.busy": "2026-08-19T03:33:08.854151Z",
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"iopub.status.idle": "2026-08-19T03:33:08.857544Z",
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"shell.execute_reply": "2026-08-19T03:33:08.857049Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ValueError: `color='red'` is ambiguous: it is a valid matplotlib color name AND a column name in element 'blobs_circles'. Disambiguate by either passing an unambiguous color form (hex string like '#ffa500' or an RGB(A) tuple), or by renaming the column.\n"
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]
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}
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],
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"source": [
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"circles = sdata[\"blobs_circles\"]\n",
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"circles[\"red\"] = circles[\"radius\"] # a column whose name is also a colour\n",
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"try:\n",
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" sdata.pl.render_shapes(\"blobs_circles\", color=\"red\").pl.show()\n",
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"except ValueError as e:\n",
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" print(\"ValueError:\", e)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "555854a5",
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"metadata": {},
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"source": [
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"## 3. Invalid image channel\n",
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"## 4. Invalid image channel\n",
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"\n",
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"Selecting a channel that does not exist raises a `ValueError` that lists the valid channels — helpful\n",
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"when you are unsure how a multichannel image is indexed (see the *Multichannel & fluorescence images*\n",
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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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"execution_count": 6,
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"id": "b1164416",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.739419Z",
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"iopub.status.busy": "2026-08-18T23:00:46.739308Z",
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"iopub.status.idle": "2026-08-18T23:00:46.741767Z",
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"shell.execute_reply": "2026-08-18T23:00:46.741290Z"
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"iopub.execute_input": "2026-08-19T03:33:08.858839Z",
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"iopub.status.busy": "2026-08-19T03:33:08.858735Z",
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"iopub.status.idle": "2026-08-19T03:33:08.861474Z",
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"shell.execute_reply": "2026-08-19T03:33:08.861008Z"
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}
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},
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"outputs": [
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"id": "bac6ece4",
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"metadata": {},
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"source": [
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"## 4. A per-channel `norm` list of the wrong length\n",
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"## 5. A per-channel `norm` list of the wrong length\n",
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"\n",
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"When you pass a list of norms for an image, its length must match the number of channels you are\n",
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"rendering (see the *Normalization and contrast* 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": 5,
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"execution_count": 7,
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"id": "50f8a28b",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.743101Z",
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"iopub.status.busy": "2026-08-18T23:00:46.742992Z",
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"iopub.status.idle": "2026-08-18T23:00:46.745491Z",
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"shell.execute_reply": "2026-08-18T23:00:46.745025Z"
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"iopub.execute_input": "2026-08-19T03:33:08.862734Z",
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"iopub.status.busy": "2026-08-19T03:33:08.862642Z",
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"iopub.status.idle": "2026-08-19T03:33:08.865037Z",
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"shell.execute_reply": "2026-08-19T03:33:08.864515Z"
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}
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},
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"outputs": [
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"id": "4d06836d",
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"metadata": {},
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"source": [
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"## 5. `grayscale` needs exactly three channels\n",
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"## 6. `grayscale` needs exactly three channels\n",
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"\n",
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"`grayscale=True` collapses a three-channel selection into one intensity, so it requires exactly three\n",
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"channels."
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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": 6,
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"execution_count": 8,
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"id": "b77803c7",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.746983Z",
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"iopub.status.busy": "2026-08-18T23:00:46.746876Z",
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"iopub.status.idle": "2026-08-18T23:00:46.896268Z",
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"shell.execute_reply": "2026-08-18T23:00:46.895864Z"
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"iopub.execute_input": "2026-08-19T03:33:08.866284Z",
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"iopub.status.busy": "2026-08-19T03:33:08.866186Z",
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"iopub.status.idle": "2026-08-19T03:33:09.025021Z",
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"shell.execute_reply": "2026-08-19T03:33:09.024560Z"
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"outputs": [
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"id": "52c83cb4",
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"metadata": {},
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"source": [
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"## 6. Invalid `PercentileNormalize` bounds\n",
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"## 7. Invalid `PercentileNormalize` bounds\n",
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"\n",
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"Percentile bounds are validated at construction time: they must satisfy `0 <= pmin < pmax <= 100`."
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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": 7,
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"execution_count": 9,
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"id": "c5293c63",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.897867Z",
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"iopub.status.busy": "2026-08-18T23:00:46.897752Z",
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"iopub.status.idle": "2026-08-18T23:00:46.900467Z",
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"shell.execute_reply": "2026-08-18T23:00:46.899901Z"
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"iopub.execute_input": "2026-08-19T03:33:09.026804Z",
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"iopub.status.busy": "2026-08-19T03:33:09.026686Z",
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"iopub.status.idle": "2026-08-19T03:33:09.029442Z",
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"shell.execute_reply": "2026-08-19T03:33:09.028925Z"
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}
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"outputs": [
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}
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],
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"source": [
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"for bad in [(50, 50), (90, 10), (-1, 50), (0, 101)]:\n",
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"bad_bounds = [\n",
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" (50, 50), # pmin == pmax (must be strictly increasing)\n",
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" (90, 10), # pmin > pmax\n",
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" (-1, 50), # pmin < 0\n",
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" (0, 101), # pmax > 100\n",
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"]\n",
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"for bad in bad_bounds:\n",
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" try:\n",
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" PercentileNormalize(*bad)\n",
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" except ValueError as e:\n",
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"`spatialdata-plot` fails fast with messages that name the offending element, column, channel, or\n",
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"bound:\n",
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"\n",
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"- **`AttributeError: ... has no attribute 'pl'`** — you forgot `import spatialdata_plot`.\n",
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"- **Element not found** — check the key in `sdata`.\n",
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"- **No column to colour by** — put the value on the element or its annotating table.\n",
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"- **Ambiguous colour/column name** — pass a hex/RGB(A) colour, or rename the column.\n",
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"- **Invalid channel** — the message lists the valid channels.\n",
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"- **Wrong-length `norm` list** — one norm per rendered channel.\n",
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"- **`grayscale` needs three channels** — select exactly three.\n",
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"id": "384e30e6",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-08-18T23:00:46.901803Z",
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"iopub.status.busy": "2026-08-18T23:00:46.901692Z",
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"iopub.status.idle": "2026-08-18T23:00:46.933690Z",
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"shell.execute_reply": "2026-08-18T23:00:46.933162Z"
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"iopub.execute_input": "2026-08-19T03:33:09.030827Z",
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"iopub.status.busy": "2026-08-19T03:33:09.030712Z",
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"iopub.status.idle": "2026-08-19T03:33:09.058691Z",
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"shell.execute_reply": "2026-08-19T03:33:09.058073Z"
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},
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"outputs": [

‎pr-22/_static/documentation_options.js‎

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const DOCUMENTATION_OPTIONS = {
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VERSION: '0.1.dev1+g375c17330.d20260818',
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VERSION: '0.1.dev1+g375c17330.d20260819',
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LANGUAGE: 'en',
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COLLAPSE_INDEX: false,
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BUILDER: 'html',

‎pr-22/api.html‎

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<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=90905a2f556bf617f1a9" />
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<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=90905a2f556bf617f1a9" />
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<script src="_static/documentation_options.js?v=6ef967b8"></script>
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<script src="_static/documentation_options.js?v=d505e5a5"></script>
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<script src="_static/sphinx_highlight.js?v=6ffebe34"></script>
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<link rel="prev" title="Interactive region annotation" href="notebooks/examples/interactive_annotate.html" />
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<meta name="viewport" content="width=device-width, initial-scale=1"/>
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<meta name="docsearch:language" content="en"/>
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<meta name="docsearch:version" content="0.1.dev1+g375c17330.d20260818" />
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<meta name="docsearch:version" content="0.1.dev1+g375c17330.d20260819" />
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‎pr-22/changelog.html‎

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<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=90905a2f556bf617f1a9" />
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<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=90905a2f556bf617f1a9" />
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<script src="_static/documentation_options.js?v=6ef967b8"></script>
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<link rel="prev" title="Plotting (.pl)" href="plotting.html" />
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<meta name="viewport" content="width=device-width, initial-scale=1"/>
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<meta name="docsearch:language" content="en"/>
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<meta name="docsearch:version" content="0.1.dev1+g375c17330.d20260818" />
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‎pr-22/contributing.html‎

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<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=90905a2f556bf617f1a9" />
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<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=90905a2f556bf617f1a9" />
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<link rel="prev" title="Changelog" href="changelog.html" />
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<meta name="docsearch:version" content="0.1.dev1+g375c17330.d20260818" />
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‎pr-22/gallery.html‎

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<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=90905a2f556bf617f1a9" />
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<link rel="prev" title="spatialdata-plot: rich static plotting from SpatialData objects" href="index.html" />
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