Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI

In this slide deck we learn how to write reproducible bio-image analysis code in Jupyter notebooks. Goal is not just to have code running elsewhere reproducibly, but also enabling others to understand workflows to enable them reproducing the analysis also in their mind and potentially other tools. Additionally we cover how to generate Jupyter notebooks from Napari and using artificial intelligence, namely bia-bob.

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2025-09-09
DOI
https://doi.org/10.5281/zenodo.16793738
Primary Topic
Cell Image Analysis Techniques
Type
article
Field-Weighted Citation Impact
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article

Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI

Zenodo (CERN European Organization for Nuclear Research)
Cell Image Analysis Techniques
article

Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI

article en

Abstract

In this slide deck we learn how to write reproducible bio-image analysis code in Jupyter notebooks. Goal is not just to have code running elsewhere reproducibly, but also enabling others to understand workflows to enable them reproducing the analysis also in their mind and potentially other tools. Additionally we cover how to generate Jupyter notebooks from Napari and using artificial intelligence, namely bia-bob.

Zenodo (CERN European Organization for Nuclear Research)
Center for Scalable Data Analytics and Artificial Intelligence (DE), Leipzig University (DE)
Openalex Percentile: Top 70%
Cell Image Analysis Techniques
DOIOpen Access PDFOpenAlex
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Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI · Zenodo (CERN European Organization for Nuclear Research) (2025) | TGRS Research Map | TGRS