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Merge pull request #99 from sebi06/work_in_progress
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2 parents f563476 + d71033c commit 013a3a2

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‎.github/workflows/test_and_deploy.yml‎

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strategy:
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matrix:
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platform: [ubuntu-latest, windows-latest]
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python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', ]
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python-version: ['3.10', '3.11', '3.12', '3.13']
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- uses: actions/checkout@v4

‎.github/workflows/test_and_deploy_testpypi.yml‎

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platform: [ubuntu-latest, windows-latest]
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python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
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python-version: ['3.10', '3.11', '3.12', '3.13']
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- uses: actions/checkout@v4

‎data/S3_1Pos_2Mosaic_T1_Z1_CH1.czi‎

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‎data/w96_A1+A2_planetable.csv‎

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;Subblock;S;M;T;C;Z;X[micron];Y[micron];Z[micron];Time[s];xstart;ystart;width;height
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0;0;0;0;0;0;0;4261.284;8361.406;683.0;0.0;0;0;1960;1416
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1;1;1;0;0;0;0;13293.666;8372.441;683.934;2.376;19758;24;1960;1416

‎demo/notebooks/omezarr_from_czi_5d.ipynb‎

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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ZARR Verion: 3.1.0 NGFF-ZARR Version: 0.15.0\n"
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"ZARR Verion: 3.1.1 NGFF-ZARR Version: 0.16.1\n"
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]
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}
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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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"F:\\Github\\czitools\\data\\CellDivision_T3_Z5_CH2_X240_Y170.ome.zarr\n"
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"/datadisk1/Github/czitools/data/CellDivision_T3_Z5_CH2_X240_Y170.ome.zarr\n"
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}
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],
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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": "c17689de830e4c74b443b5544c3610e5",
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"model_id": "b0087b111b7248de9e456bb662f75d3e",
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"version_major": 2,
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"version_minor": 0
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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": "f9353554723246e2b63c91bc218967ef",
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"model_id": "b7a21676cc0c4d659417a073ec8b5822",
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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": "0cb914978813439ea5b96cba2b6d9787",
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"model_id": "14a2b4e5d47e4f3c98521409cfb8f130",
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "c670b17c",
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"metadata": {},
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "24a93ccf-5cd4-4435-867b-190093bba3cc",
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"metadata": {},
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‎demo/notebooks/read_czi_metadata.ipynb‎

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"cells": [
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{
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"execution_count": 1,
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"metadata": {},
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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": "908516cbc84c4feba61befc923e0459e",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"FileChooser(path='/datadisk1/Github/czitools/data', filename='', title='', show_hidden=False, select_desc='Sel…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"if not IN_COLAB:\n",
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" # choose local file\n",
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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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"Selected File: /datadisk1/Github/czitools/data/w96_A1+A2.czi\n"
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]
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}
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],
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"if not IN_COLAB:\n",
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},
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{
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"cell_type": "code",
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"metadata": {},
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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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"SizeS: 2\n",
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"SizeT: None\n",
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"SizeZ: None\n",
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"SizeC: 2\n",
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"SizeY: 1440\n",
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"SizeX: 21718\n"
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]
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}
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],
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"# get only specific metadata\n",
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"czi_dimensions = czimd.CziDimensions(filepath)\n",
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},
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"execution_count": 9,
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"outputs": [],
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"outputs": [
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "73ee49cd6a0d4e6f9682099239068919",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"VBox(children=(Output(layout=Layout(height='300px')),))"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"# get the complete metadata at once as one big class\n",
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"mdata = czimd.CziMetadata(filepath)\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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"metadata": {},
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"outputs": [],
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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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"XML File written to: /datadisk1/Github/czitools/data/w96_A1+A2_CZI_MetaData.xml\n"
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]
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}
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],
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"source": [
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"# write XML to disk\n",
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"xmlfile = czimd.writexml(filepath)\n",
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"metadata": {},
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"outputs": [],
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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": "4a0b8eebdabc4b0398d7dc59a79132e3",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Reading sublocks planes: 0 2Dplanes [00:00, ? 2Dplanes/s]"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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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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"\u001b[32m2025-08-23 19:59:24,011 - czitools - INFO - Planetable saved successfully at: /datadisk1/Github/czitools/data/w96_A1+A2_planetable.csv\u001b[0m\n"
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]
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},
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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": "0c9fc900a4454598ab504be5ba752c7b",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"VBox(children=(Output(layout=Layout(height='300px')),))"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"# get the planetable for the CZI file\n",
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"pt, savepath = misc.get_planetable(filepath,\n",

‎demo/notebooks/read_czi_metadata_marimo.py‎

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import marimo
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__generated_with = "0.14.11"
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__generated_with = "0.14.17"
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app = marimo.App()
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