A number of open source image analysis software packages are available on our computers. Other open source packages can be installed on demand. Most of our computers are equipped for 3D/4D processing and also for training and applying deep learning solutions. If you need help with a open source image analysis software please contact us.

Cell profiler

Software for quantitative image analysis and task automation. No programming skills are required, the software works via the creation of image analysis pipelines.

FIJI / ImageJ

2D and 3D image processing and analysis software. Extensible via macros (IJ-macro language), scripts (python, javascript, ...)  and plugins (java).

  • Available on all workstations of the facility.
  • ImageJ/Fiji

Flowing Software

 Flowing Software is a free flow cytometry data analysis software for Windows. The project combines high throughput data analysis with flowing usability. The easy-to-use visual interface ensures an effective data analysis with your personal computer!


2D et 3D image processing and analysis software. Build on plugins, icy also provides the possibility to create ones own analysis protocols using visual programming. Scripts can be written in python and javascript.


ILASTIK is an easy to use, open source, machine learning software. Different machine learning modules for segmentation (pixel classification), object classification and counting are available


From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access.