University of Heidelberg

03/25/2024 Open Position

The BMCV group currently offers a PhD position in biomedical image analysis.

More details can be...

03/01/2023 Publication in IEEE Transactions on Pattern Analysis and Machine Intelligence 2023

Our article "Superadditivity and Convex Optimization for Globally Optimal Cell Segmentation Using...

01/27/2018 Cell Tracking Challenge, Nature Methods 2017

The cell tracking method of the BMCV group yielded top-ranking results in an international...

07/13/2015 ISBI 2016

Karl Rohr is program chair of the IEEE International Symposium on Biomedical Imaging (ISBI) which...

11/10/2014 Project QuantVessel at Deutsche Bundestag (German Parliament)

The research project QuantVessel of the BMCV group is presented at an exhibition of the German...

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Galaxy Image Analysis

The BMCV Group is developing workflows and tools for web-based analysis of microscopy image data and systematic phenotyping of human cells. We developed Galaxy Image Analysis as extension of the Galaxy platform to address the requirements of microscopy image analysis. Workflows and tools for automated extraction of cellular phenotypes are integrated and deployed by Bioconda. Selected workflows are integrated within ELIXIR services like Galaxy Europe. Tools and workflows are also provided under GitHub. We use Galaxy Image Analysis in different interdisciplinary cooperations. The work is carried out within HD-HuB of the de.NBI project. Below is a list our contributions.

Galaxy Tools (Examples)

Workflows (Examples)

  • RNAi screen analysis
  • Capturing mitoflashes
  • MALDI & HE co-registration
  • Registration of images based on landmarks
  • Registration of images based on intensity information
  • Spot tracking
  • Segmentation

Galaxy Interactive Environments

Bioconda Packages

Conda Forge Packages


  • Image datatypes support
  • Polygon datatypes support
  • Several bugfixes (e.g., UI, scheduling, core)

Galaxy Docker

  • Several bugfixes

Galaxy Docker Imaging Flavour

  • Recipe maintenance
  • Tool selection

Galaxy Jupyter GIE

  • Several bugfixes

Galaxy Ansible

  • Several bugfixes


  • Several bugfixes

Galaxy Training Network

  • Tutorial on basics in Galaxy Image Analysis
  • Tutorial on RNAi screen analysis

Contact: E-Mail (Last update: 18/03/2024)