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@BiAPoL

Bio-image Analysis group at the DFG Cluster of Excellence "Physics of Life" at TU Dresden

README.md

Bio-image analysis technology development group (BiAPoL)

An image analysis group with expertise in Machine Learning who got your back and your pixels

Welcome to the profile of the bio-image analysis technology development group (BiAPoL) at Physics of Life / TU Dresden. We provide services and tools for the analysis of microscopy images in the life sciences. If you have any questions or need help with image analysis, feel free to contact us (see contact information below).

Services
Consultation

Image Data Science Consulting


We provide services for the analysis of microscopy images in the life sciences
  1. Method Exploration
  2. Pair Programming
Consultation

Internship/mini-sabbaticals Development


Stay with us to bolster your analysis and code proficiency
  1. 2-4 weeks lab rotation for a focused bio-image analysis task
  2. Turn images into knowledge

Consultation

Plugin/library development


Make your code sustainable and reusable
  1. FAIRness
  2. Napari plugins, Fiji plugins, Jupyter notebooks or Python libraries (i.e., PyPi)
Consultation

Rent-a-scientist


Pay us to support your work
  1. Organize workshops or other teaching events
  2. Get the help of a professional image data scientist for your project to make a leap forward.

Members

We are currently three postdocs and one student working in the group:
Marcelo

Marcelo Zoccoler (Postdoc)


Interested in Image + Signal Processing, Fluorescence Lifetime-based Segmentation, Time-lapse Signal Classification, Machine Learning, Software and Plugin Development @zoccoler

Johannes

Johannes Soltwedel (Postdoc)


Interested in segmentation, machine/deep learning, algorithms, teaching, surface meshes and geometry.

@jo-mueller
Stefan

Stefan Hahmann (Postdoc)


Interested in Research Software Engineering, Fiji Plugins, Feature Extraction, Deep Learning, Classification, Graphs, Open Source.

@stefanhahmann
Maleeha

Maleeha Hassan (Student)


Interested in Image Analysis, Machine Learning, meshes and cancer organoids.

@maleehahassan

Repositories by Category

After clicking one of the categories below, scroll down the webpage to find the filtered repositories.

Contact

For more information on our current and previous members and our mission, visit our group page. For requests, please contact us via email (biapol (at) tu-dresden.de). For image analysis questions, please make sure to also check the image analysis forum.

Please understand that, regarding image analysis, our first and foremost responsibilities are to the Physics of Life institute and the Dresden Life Science community. We will try to help you as much as possible, but we may not be able to provide immediate support.

Popular repositories Loading

  1. Bio-image_Analysis_with_Python Bio-image_Analysis_with_Python Public

    Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecular and Cellular Bioengineering (CMCB) / University of Techn…

    Jupyter Notebook 205 50

  2. napari-clusters-plotter napari-clusters-plotter Public

    A napari plugin for clustering objects according to their properties.

    Jupyter Notebook 82 11

  3. PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis Public

    PoL Bioimage Analysis Training School: GPU-Accelerated Image Analysis Track

    Cool 25 9

  4. imagej-macro-cheat-sheet imagej-macro-cheat-sheet Public

    19 2

  5. Quantitative_Bio_Image_Analysis_with_Python_2022 Quantitative_Bio_Image_Analysis_with_Python_2022 Public

    This repository hosts notebooks, information and data for the Quantitative Bio-Image Analysis with Python Course 2022.

    Shell 15 3

  6. Image-data-science-with-Python-and-Napari-EPFL2022 Image-data-science-with-Python-and-Napari-EPFL2022 Public

    Cool 15 8

Repositories

Showing 10 of 40 repositories
  • napari-clusters-plotter Public

    A napari plugin for clustering objects according to their properties.

    BiAPoL/napari-clusters-plotter’s past year of commit activity
    Jupyter Notebook 82 BSD-3-Clause 11 35 9 Updated Mar 31, 2025
  • .github Public
    BiAPoL/.github’s past year of commit activity
    1 0 1 0 Updated Mar 25, 2025
  • biaplotter Public

    A base napari plotter widget for interactive plotting

    BiAPoL/biaplotter’s past year of commit activity
    Python 7 BSD-3-Clause 2 5 2 Updated Mar 21, 2025
  • TrendsInMicroscopy_2025 Public

    Image analysis workshop at TrendsInMicroscopy2025

    BiAPoL/TrendsInMicroscopy_2025’s past year of commit activity
    0 CC-BY-4.0 0 0 0 Updated Mar 19, 2025
  • blog Public

    Most of us study and work at the Bio-image Analysis Technology Development group at the DFG Cluster of Excellence “Physics of Life” at the TU Dresden. We blog about image data science, knowledge exchange and research data management in the life sciences.

    BiAPoL/blog’s past year of commit activity
    14 CC-BY-4.0 8 8 3 Updated Mar 14, 2025
  • omero-tools Public

    Example notebooks and tricks to interact with OMERO from Python

    BiAPoL/omero-tools’s past year of commit activity
    4 GPL-2.0 0 0 1 Updated Mar 12, 2025
  • DIGS-BB_LM_Course_Bio-Image_Analysis_2024 Public
    BiAPoL/DIGS-BB_LM_Course_Bio-Image_Analysis_2024’s past year of commit activity
    0 CC-BY-4.0 0 0 0 Updated Sep 18, 2024
  • BioImage-Analysis-and-Data-Processing-Workshop-2024 Public

    This repository hosts material for the BioImage Analysis and Data Processing Workshop 2024, which takes place in VMCF Microscopy Facility, Vinicna 7, Prague, Czechia

    BiAPoL/BioImage-Analysis-and-Data-Processing-Workshop-2024’s past year of commit activity
    Shell 4 CC-BY-4.0 1 0 0 Updated Aug 8, 2024
  • napari-clusters-plotter-example-notebooks Public

    This repository hosts jupyter notebooks with examples of napari-clusters-plotter usage

    BiAPoL/napari-clusters-plotter-example-notebooks’s past year of commit activity
    Jupyter Notebook 3 BSD-3-Clause 2 1 1 Updated Jun 13, 2024
  • PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis Public

    PoL Bioimage Analysis Training School: GPU-Accelerated Image Analysis Track

    BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis’s past year of commit activity
    Cool 25 CC-BY-4.0 9 0 0 Updated Jun 5, 2024
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