Image Analysis

Image processing and analysis

The General Instrumentation department provides support in image management, processing and analysis either with the implementation of custom-made software (macros in ImageJ) or with training of individual users at the following software available:

ImageJ / FIJI

Powerful freeware software for image manipulation and analysis. Contains a huge variety of plugins and also gives the possibility of custom-made analysis macros implementation

Huygens Essential

Deconvolution software from SVI with modules for deconvolution of confocal and widefield images.

Imaris Viewer

Freeware from Bitplane for 3D renderings.


Acquisition and handling of images acquired with a Leica microscope. Various versions of this software are installed in microscope PCs including modules like the 3D module for 3D rendering of z-stacks and Lightning and Thunder modules for computational clearing of confocal and widefield acquisitions.


Software (cygwin, etomo, 3dmod, drawing tools, PEET, Serial/cryo-EM), guides and tutorials for cryo-EM and (cryo) tomography TEM, alignment and modeling.

OMERO (experimental)

An experimental version of the powerful data management system runs on a limited storage server. The OMERO can handle all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 140 image file formats supported, including all major microscope formats.