General image analysis

If you have questions, problems or projects in image analysis, please contact Image Analysis Support.

Analysis workstations

We offer several virtual workstations in the EMBL 3D cloud ('gold' and 'silver' versions ) and dedicated image analysis workstations.

Software packages available on our workstations include:

  • CellProfiler: Open source software for batch analysis of large microscopy data sets.
  • CellCognition: Open source software for automated cell segmentation and classification using machine learning. Cellcognition supports batch analysis of large datasets.
  • Fiji (ImageJ): Open source image analysis software with large user and developer community. Available on all workstations.
  • Huygens Remote Manager (HRM, SVI): Server-based deconvolution of 3D data sets. See our short step-by-step manual, the how to deconvolve with HRM at EMBL or the full manual.
  • Imaris (Bitplane / Andor): Commercial 4D analysis and visualization tool. We offer several floating licenses.

Useful downloads


The ALMF and Center for Bioimage Analysis (CBA) team up to run a number of image analysis training courses (ALMF courses, CBA upcoming events), both regular and on demand. These include:

  • Basic FIJI/Image J training, offered as part of our Basics in Microscopy courses. Additional FIJI training is provided by the CBA.
  • Introduction to Cellprofiler.

Training for other topics in image analysis and microscope automation can be arranged on demand, please contact image-analysis-support.

Data and Image Analysis Support

We offer basic support in image analysis and statistical data analysis to our external visitors for the screens that they carry out during their visit.

More general and advanced image analysis and statistical data analysis support are provided by the EMBL Centre for Molecular and Cellular Imaging and the EMBL Centre for Statistical Data Analysis, respectively.

High-throughput analysis on EMBL computing cluster

For batch-analysis of large amounts of data we support distributed computing on the EMBL computing cluster.

For batch image analysis we currently provide a cluster workflow for CellProfiler for analysing high-throughput microscopy data generated at ALMF.

For statistical analysis and visual browsing of the output generated by high-throughput image analysis results we provide the open source HTM R-package developed by Christian Tischer.

Related EMBL services

Complementary image analysis and statistical data analysis support also is provided by the EMBL Centre for Molecular and Cellular Imaging and the EMBL Centre for Statistical Data Analysis, respectively.

Slides for data analysis and image processing

Stefan Terjung: Basics in Image Processing

Yury Belyaev: Rendering and analysis of confocal datasets