Centre for Bioimage Analysis

Centre for Bioimage Analysis

The Centre for Bioimage Analysis (CBA) supports scientists in extracting quantitative information from images acquired with light- or electron-microscopy.

Support is provided on various aspects of image analysis, such as
- image data handling
- quantitative image interpretation and visualisation
- image registration
- object segmentation and tracking
- morphological and intensity quantifications.

The CBA closely collaborates with the Advanced Light Microscopy Facility (ALMF) and the Electron Microscopy Core Facility (EMCF) in order to ensure optimal image acquisition modalities for downstream quantitative analysis.

Together with ALMF, EMCF and EMBL’s IT department, the CBA provides access to dedicated image analysis software, running on high-performance virtual workstations and the high performance compute cluster.

In addition to project specific consultancy, the CBA also offers regular courses on image analysis in general and on how to use particular software packages such as ImageJ, CellProfiler and Imaris. Upcoming courses can be found here.

For bioimage analysts spread across EMBL research units, the CBA serves also as a platform to share developments, exchange expertise, and learn about advances and new approaches in computational image analysis.

Best practice

Please always follow best practices of bioimage analysis, otherwise you run a severe risk of obtaining erroneous results.

One-on-one consultancy

To schedule a one-on-one consultancy session (typically 1.5 hours), please send a mail to image-analysis-support@embl.de. To make the consultancy most effective, please prepare representative example images according to these guidelines.

Drop-in sessions

If you are already able to conduct image analysis on your own, but perfer to work in company or would like to have some discussions, you are welcome to join the weekly bioimage analysis drop-in sessions. The sessions are every Thursday 10:00 - 12:00 in room 13-518 (please note that due to conferences or other events it is not always guarantueed that CBA staff will be present).

MOIA seminar series

The MOIA seminar series are a platform for discussion of developments related to microscopy, optics and image analysis (MOIA). Everyone is free to present their project, ideas, developments, obstacles, or interesting publications. If you would like to to present, please send a mail to moia-seminars@embl.de.


Online training
Online resources
  • Resources for teaching image analysis in ImageJ (github)
  • Concept based language agnostic image analysis training resources (gitlab)
    • with Toby Hodges (EMBL)
    • we are looking for co-workers! Please contact us if you would like to contribute!

Software development

  • MultiModalBrowser: Multi-modal remote big image data browsing (publication, github).
  • BigDataProcessor2: Big image data processing in ImageJ (github).
    • co-developed by Ashis Ravindran (former intern at CBA)
    • conceptual input from Nils Norlin (EMBL)
  • BigDataViewer-Playground: Correlative big image data registration and visualisation (github).
    • co-developed with Nicolas Chiaruttini (EPFL)
    • conceptual input from Matrin Schorb (EMBL)
CBA related
  • shinyHTM: (High-throughput) image analysis results visualisation and quality control (github).
    • mainly developed by Hugo Bothelo, University of Lisbon, Portugal
    • contributions from CBA and Aliaksandr Halavatyi (ALMF)
    • conceptual input from Sabine Reither and Beate Neumann (ALMF)
  • Image Data Explorer: Image analysis results visualisation and quality control (github).
    • mainly developed by Jean Karim Heriche, EMBL Heidelberg
    • conceptual input from CBA


Image Analysis Support
Christian Tischer