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  • Pro

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@conda-forge @Kainmueller-Lab @betaseg @ida-mdc @album-app @brain-tools @polarityjam

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jpalbrecht/README.md

Scientist at Helmholtz Imaging, Max Delbrück Center (MDC), Berlin. I design open-source software that makes scientific image analysis reusable and replicable, and I develop image-analysis methods that include machine learning. Currently I am exploring how LLM agents can orchestrate verified, executable tools while every step stays reproducible.

Projects

  • Album: framework for sharing and replicably running scientific routines, each in its own environment. Owner and architect; maintainer of the conda-forge package. Code on GitLab · arXiv:2110.00601
  • Polarity-JaM: toolbox for cell polarity, junction and morphology quantification, with a napari plugin and an R/Shiny web app. Software architect and project co-lead. Nature Communications 2025
  • ARI3D: interactive quantification of regions in 3D X-ray CT images. Architect and lead developer. arXiv:2508.09849

Album and ARI3D live on GitLab, where most of my development happens: gitlab.com/jpalbrecht91.

I also run the programming exercises and tutorials of the course Machine Learning for Image Analysis at HU Berlin and HPI.

ORCID · Google Scholar · LinkedIn · github@jpalbrecht.de

Pinned Loading

  1. album-app/album album-app/album Public

    Mirror of gitlab.com/album-app/album: framework for sharing and replicably running scientific routines, website https://album.solutions

    Python 3

  2. polarityjam/polarityjam polarityjam/polarityjam Public

    The feature extraction pipeline lets you extract relevant features from your image(s) and collect them in a csv file.

    Python 6 3

  3. volkamerlab/ai_in_medicine volkamerlab/ai_in_medicine Public

    Jupyter Notebook 38 10

  4. Kainmueller-Lab/ACTIS Kainmueller-Lab/ACTIS Public

    Python 2