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 one hour), 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.

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 teaching material

Software developments

  • NEUBIAS bioimage analysis training resources (git repo): Community platform for sharing bioimage analysis training resources. Developers: Toby Hodges (The Carpentries), Christian Tischer (EMBL), Antonio Politi (MPI Biophysical Chemistry)

  • MoBIE (publication, git repo): Fiji plugin for exploration and annotation of multi-modal cloud hosted big image data. Developers: Christian Tischer (EMBL), Constantin Pape (EMBL), Kimberly Meechan (EMBL), Martin SchorbEMBL)

  • BigDataProcessor2 (publication, git repo): Fiji plugin for big image data processing. Developers: Christian Tischer (EMBL), Ashis Ravindran (Heidelberg University), Sabine Reither (EMBL), Nils Norlin (Lund University), Nicolas Chiaruttini (EPFL)

  • PlateViewer (git repo): Fiji plugin for visual inspection of multi-well high throughput microscopy image data. Developers: Christian Tischer (EMBL), Constantin Pape (EMBL), Adrian Wolny (EMBL)

  • ElastixWrapper (git repo): Fiji plugin for 3D image registration with elastix. Developers: Christian Tischer (EMBL), Kimberly Meechan (EMBL)

  • CATS (git repo): Fiji plugin for context aware trainable segmentation of big image data. Developers: Christian Tischer (EMBL)

  • Spindle3D: Fiji plugin for automated measurement of 3D morphological parameters of volumetric images of mitotic spindles (git repo). Developers: Christian Tischer (EMBL), Tobias Kletter (HU Berlin)

  • BigDataViewer-Playground: Fiji plugin for correlative big image data registration and visualisation (git repo). Developers: Nicolas Chiaruttini (EPFL), Christian Tischer (EMBL), Matrin Schorb (EMBL)

  • shinyHTM (git repo): R shiny app for high-throughput microscopy analysis results visualisation and quality control ). Developers: Hugo Botelho (University of Lisbon, Portugal), Christian Tischer (EMBL), Aliaksandr Halavatyi (EMBL), Sabine Reither (EMBL), Beate Neumann (EMBL)

  • Image Data Explorer (git repo): R shiny app for image analysis results visualisation and quality control. Developers: Jean Karim Heriche (EMBL), Coralie Muller (Université de Bordeaux)


Image Analysis Support