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Title: GitHub - zeissmicroscopy/ZEN_API_Python_CZI_workshop: Material to showcase and test several tools and packages releated to ZEN, CZI image files and python packages related to those topics · GitHub

Open Graph Title: GitHub - zeissmicroscopy/ZEN_API_Python_CZI_workshop: Material to showcase and test several tools and packages releated to ZEN, CZI image files and python packages related to those topics

X Title: GitHub - zeissmicroscopy/ZEN_API_Python_CZI_workshop: Material to showcase and test several tools and packages releated to ZEN, CZI image files and python packages related to those topics

Description: Material to showcase and test several tools and packages releated to ZEN, CZI image files and python packages related to those topics - zeissmicroscopy/ZEN_API_Python_CZI_workshop

Open Graph Description: Material to showcase and test several tools and packages releated to ZEN, CZI image files and python packages related to those topics - zeissmicroscopy/ZEN_API_Python_CZI_workshop

X Description: Material to showcase and test several tools and packages releated to ZEN, CZI image files and python packages related to those topics - zeissmicroscopy/ZEN_API_Python_CZI_workshop

Opengraph URL: https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop

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direct link

Domain: github.com

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aihttps://github.com/topics/ai
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pylibczirwhttps://github.com/topics/pylibczirw
pythonhttps://github.com/topics/python
scriptinghttps://github.com/topics/scripting
segmentationhttps://github.com/topics/segmentation
zenhttps://github.com/topics/zen
zen-apihttps://github.com/topics/zen-api
zenapihttps://github.com/topics/zenapi
Readmehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#readme-ov-file
GPL-3.0 licensehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#GPL-3.0-1-ov-file
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README.mdhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/README.md
README.mdhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/README.md
pyproject.tomlhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/pyproject.toml
pyproject.tomlhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/pyproject.toml
READMEhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop
GPL-3.0 licensehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#smart-microscopy-on-site-workshop-from-zero-to-hero-with-zen-and-open-source-tools
Smart Microscopy On-site Workshop: From Zero to Hero with ZEN and Open-Source Toolshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#smart-microscopy-on-site-workshop-from-zero-to-hero-with-zen-and-open-source-tools
Disclaimerhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#disclaimer
General Remarkshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#general-remarks
Prerequisiteshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#prerequisites
Install python base environment (miniconda etc.)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#install-python-base--environment-miniconda-etc
ZEN APIhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api
ZEN API - General Informationhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api---general-information
ZEN API - ZEN Blue 3.12 - Documentationhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api---zen-blue-312---documentation
ZEN API Python Exampleshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api-python-examples
ShowCase: Pixel Stream and Online Processinghttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#showcase-pixel-stream-and-online-processing
ShowCase: Guided Acquisitionhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#showcase-guided-acquisition
Deep Learning Topicshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#deep-learning-topics
Train a Deep-Learning Model for Semantic Segmentation on arivis Cloudhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-a-deep-learning-model-for-semantic-segmentation-on-arivis-cloud
Use the model in your python codehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#use-the-model-in-your-python-code
Train your own model and package (as *.czann) using the czmodel packagehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-your-own-model-and-package-as-czann-using-the-czmodel-package
Train a simple model for semantic segmentationhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-a-simple-model-for-semantic-segmentation
Train a simple model for regressionhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-a-simple-model-for-regression
Use the model inside Napari (experimental)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#use-the-model-inside-napari-experimental
Using the czitools package (experimental)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#using-the-czitools-package-experimental
Read CZI metadatahttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#read-czi-metadata
Read CZI pixeldatahttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#read-czi-pixeldata
Write OME-ZARR from 5D CZI image datahttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#write-ome-zarr-from-5d-czi-image-data
Write CZI using ZSTD compressionhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#write-czi-using-zstd-compression
Show planetable of a CZI image as surfacehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#show-planetable-of-a-czi-image-as-surface
Read a CZI and segment using Voroni-Otsu provided by PyClesperanto GPU processinghttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#read-a-czi-and-segment-using-voroni-otsu-provided-by-pyclesperanto-gpu-processing
CZICompress - Compress CZI image files from the commandlinehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czicompress---compress-czi-image-files-from-the-commandline
General usagehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#general-usage
Usage example for single files from commandline (cmd.exe)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#usage-example-for-single-files-from-commandline-cmdexe
Usage example with multiple files (bash)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#usage-example-with-multiple-files-bash
CZIShrink - Compress CZI image files from a cross-platform UIhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czishrink---compress-czi-image-files-from-a-cross-platform-ui
CZICheck - Check CZI for internal errorshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czicheck---check-czi-for-internal-errors
napari-czitools (experimental)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#napari-czitools-experimental
CZI and OME-ZARR (experimental)https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czi-and-ome-zarr-experimental
Convert CZI to OME-ZARR using ome-zarrhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-using-ome-zarr
Convert CZI to OME-ZARR using ngff-zarrhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-using-ngff-zarr
Convert CZI to OME-ZARR HCS Plate using ome-zarrhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-hcs-plate-using-ome-zarr
Convert CZI to OME-ZARR HCS Plate using ngff-zarrhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-hcs-plate-using-ngff-zarr
Useful Linkshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#useful-links
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#disclaimer
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#general-remarks
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#prerequisites
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#install-python-base--environment-miniconda-etc
Download Minicondahttps://www.anaconda.com/download/success
YML filehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/workshop/env_smartmic.yml
arivis Cloudhttps://www.arivis.cloud
Colabhttps://colab.research.google.com
arivis Cloudhttps://www.arivis.cloud
Docker Desktophttps://www.docker.com/products/docker-desktop
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api---general-information
ZEN API -General Informationhttps://github.com/zeiss-microscopy/OAD/blob/master/ZEN-API/README.md
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api---zen-blue-312---documentation
ZEN API Documentationhttps://github.com/zeiss-microscopy/OAD/blob/master/ZEN-API/documentation/ZEN_API_Documentation_20250509.md
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#zen-api-python-examples
ZEN API Examples - ZEN Blue 3.12https://github.com/sebi06/ZEN_Python_CZI_Smart_Microscopy_Workshop/tree/main/workshop/zen_api
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#showcase-pixel-stream-and-online-processing
zenapi_streaming.pyhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/python_examples/zenapi_streaming.py
https://raw.githubusercontent.com/zeiss-microscopy/OAD/master/ZEN-API/images/zenapi_online_process.gif
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#showcase-guided-acquisition
zenapi_guidedacq.pyhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/python_examples/zenapi_guidedacq.py
https://raw.githubusercontent.com/zeiss-microscopy/OAD/master/ZEN-API/images/zenapi_guidedacq.gif
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#deep-learning-topics
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-a-deep-learning-model-for-semantic-segmentation-on-arivis-cloud
arivis Cloudhttps://www.arivis.cloud
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/apeer_dataset_nuc.png
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/APEER_annotation_auto_background.gif
Docs - Partial Annotationshttps://docs.apeer.com/machine-learning/annotation-guidelines
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#use-the-model-in-your-python-code
https://colab.research.google.com/github/sebi06/ZEN_Python_CZI_Smart_Microscopy_Workshop/blob/main/workshop/notebooks/run_prediction_from_czann.ipynb
czmodelhttps://pypi.org/project/czmodel
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-your-own-model-and-package-as-czann-using-the-czmodel-package
PyTorchhttps://pytorch.org
ONNXhttps://onnx.ai
czmodelhttps://pypi.org/project/czmodel
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-a-simple-model-for-semantic-segmentation
https://colab.research.google.com/github/sebi06/ZEN_Python_CZI_Smart_Microscopy_Workshop/blob/main/workshop/notebooks/SingleClassSemanticSegmentation_PyTorch.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#train-a-simple-model-for-regression
https://colab.research.google.com/github/sebi06/ZEN_Python_CZI_Smart_Microscopy_Workshop/blob/main/workshop/notebooks/Regresssion_PyTorch.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#use-the-model-inside-napari-experimental
Naparihttps://github.com/napari/napari
napari-czann-segmenthttps://github.com/sebi06/napari_czann_segment
piphttps://pypi.org/project/pip/
Napari Hub - napari-czann-segmenthttps://www.napari-hub.org/plugins/napari-czann-segment
https://github.com/sebi06/napari-czann-segment/raw/main/readme_images/Train_APEER_run_Napari_CZANN_no_highlights_small.gif
czitoolshttps://pypi.org/project/czitools
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#using-the-czitools-package-experimental
czitoolshttps://pypi.org/project/czitools
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#read-czi-metadata
https://colab.research.google.com/github/sebi06/czitools/blob/main/demo/notebooks/read_czi_metadata.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#read-czi-pixeldata
https://colab.research.google.com/github/sebi06/czitools/blob/main/demo/notebooks/read_czi_pixeldata_simple.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#write-ome-zarr-from-5d-czi-image-data
https://colab.research.google.com/github/sebi06/czitools/blob/main/demo/notebooks/omezarr_from_czi_5d.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#write-czi-using-zstd-compression
https://colab.research.google.com/github/sebi06/czitools/blob/main/demo/notebooks/save_with_ZSTD_compression.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#show-planetable-of-a-czi-image-as-surface
https://colab.research.google.com/github/sebi06/czitools/blob/main/demo/notebooks/show_czi_surface.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#read-a-czi-and-segment-using-voroni-otsu-provided-by-pyclesperanto-gpu-processing
https://colab.research.google.com/github/sebi06/czitools/blob/main/demo/notebooks/read_czi_segment_voroni_otsu.ipynb
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czicompress---compress-czi-image-files-from-the-commandline
CZICompresshttps://github.com/ZEISS/czicompress
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#general-usage
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#usage-example-for-single-files-from-commandline-cmdexe
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#usage-example-with-multiple-files-bash
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/czicompress_linux_bash.gif
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czishrink---compress-czi-image-files-from-a-cross-platform-ui
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/CZIShrink_win11_running.png
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/CZIShrink_win11_badge.png
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/czishrink_linux.gif
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czicheck---check-czi-for-internal-errors
libCZIhttps://github.com/ZEISS/libczi
pylibCZIrwhttps://pypi.org/project/pylibCZIrw
pylibCZIrw_githubhttps://github.com/ZEISS/pylibczirw
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/images/czichecker1.png
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#napari-czitools-experimental
Naparihttps://github.com/napari/napari
napari-czitoolshttps://github.com/sebi06/napari-czitools
piphttps://pypi.org/project/pip/
Napari Hub - napari-czitoolshttps://napari-hub.org/plugins/napari-czitools.html
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#czi-and-ome-zarr-experimental
ome-zarrhttps://github.com/ome/ome-zarr-py
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-using-ome-zarr
write_omezarr_adv.pyhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/workshop/czi_omezarr/write_omezarr_adv.py
ngff-zarrhttps://github.com/fideus-labs/ngff-zarr
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-using-ngff-zarr
write_omezarr_adv.pyhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/workshop/czi_omezarr/write_omezarr_ngff.py
ome-zarrhttps://github.com/ome/ome-zarr-py
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-hcs-plate-using-ome-zarr
write_omezarr_adv.pyhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/workshop/czi_omezarr/write_hcs_omezarr.py
ngff-zarrhttps://github.com/fideus-labs/ngff-zarr
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#convert-czi-to-ome-zarr-hcs-plate-using-ngff-zarr
write_omezarr_adv.pyhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/blob/main/workshop/czi_omezarr/write_hcs_ngffzarr.py
https://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#useful-links
GitHubhttps://github.com/napari/napari
PyPIhttps://pypi.org/project/pip/
PyPIhttps://pypi.org/
PyPIhttps://pypi.org/project/pylibCZIrw
GitHubhttps://github.com/ZEISS/pylibczirw
PyPIhttps://pypi.org/project/czmodel
PyPIhttps://pypi.org/project/cztile
arivis Cloudhttps://www.arivis.cloud
GitHubhttps://github.com/sebi06/napari_czann_segment
GitHubhttps://github.com/sebi06/napari-czitools
ZEISShttps://www.zeiss.com/microscopy/int/products/microscope-software/zen/czi.html
PyTorchhttps://pytorch.org
ONNXhttps://onnx.ai
GitHubhttps://github.com/ZEISS/libczi
PyPIhttps://pypi.org/project/czitools
Colabhttps://colab.research.google.com
Docker Desktophttps://www.docker.com/products/docker-desktop
GitHubhttps://github.com/ZEISS/czicompress
GitHubhttps://github.com/ZEISS/czicheck
GitHubhttps://github.com/ome/ome-zarr-py
NGFFhttps://ngff.openmicroscopy.org/
GitHubhttps://github.com/fideus-labs/ngff-zarr
aihttps://github.com/topics/ai
czihttps://github.com/topics/czi
czmodelhttps://github.com/topics/czmodel
deep-learninghttps://github.com/topics/deep-learning
image-analysishttps://github.com/topics/image-analysis
image-processinghttps://github.com/topics/image-processing
metadatahttps://github.com/topics/metadata
pylibczirwhttps://github.com/topics/pylibczirw
pythonhttps://github.com/topics/python
scriptinghttps://github.com/topics/scripting
segmentationhttps://github.com/topics/segmentation
zenhttps://github.com/topics/zen
zen-apihttps://github.com/topics/zen-api
zenapihttps://github.com/topics/zenapi
Readmehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#readme-ov-file
GPL-3.0 licensehttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop#GPL-3.0-1-ov-file
Activityhttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/activity
4 forkshttps://github.com/zeissmicroscopy/ZEN_API_Python_CZI_workshop/forks
Report repositoryhttps://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fzeissmicroscopy%2FZEN_API_Python_CZI_workshop&report=zeissmicroscopy+%28user%29
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

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