Image analysis software

Arivis Vision 4d

Modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited sizes independently of available RAM.


Installation: 1 x floating licence available on all workstations (book it as ‘equipment’ in addition to your workstation reservation!)


Fiji is an image processing package: a “batteries-included” distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.


A simple, user-friendly tool for interactive image classification, segmentation and analysis.

Bitplane Imaris: 3/4D Image Visualization and Analysis Software

We have 8 x Imaris 9.3 floating licences available on all our workstations. The floating licences need to be booked in PPMS as separate resources:

  1. One View, a new Arena view that performs as a microscopy image browser mirroring your internal, external, and network drive file systems.
  2. One Pipeline, improved batch processing to include image processing functions.  Perform those functions and your object wizard-based analysis within just one pipeline.
  3. Imaris file converter: (batch) convert (multiple) datasets to ‘.ims’ format. Imaris converter is integrated in imaris 9.3 or above.
  4. ClearView™ deconvolution (1x): this is an Imaris deconvolution licence: please only select this option in case you need it during your session, and don’t forget to deactivate it after your session! – please book as Special Environment 1 on the floating licence reservation in PPMS
  5. Imaris stitcher (1x): for stitching tiled image stacks – please book as Special Environment 2 on the floating licence reservation in PPMS

For your convenience, the usage of the Imaris licences can be seen here:

  • The log is updated automatically every 10 minutes
  • In case you booked it and you cannot use it, this tool helps you to identify which user is using it without booking …

Mathworks Matlab

A desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly

Wolfram Research Mathematica

Technical computing environment for arbitrary precision arithmetic and symbolic computation.


  • installation: workstation 3,4,5 and 6 – only 1 x dongle available (book it here)

SVI Huygens

Deconvolution: a mathematical operation used in Image Restoration to recover an image that is degraded by a physical process which can be described by the opposite operation, a convolution.

Packages: Huygens Professional / Widefield & Brightfield / Confocal / Spinning Disc / STED-STAB / Array Detector (Airyscan & SPAD) Optical option / Full File-readers Option / Time option / Object Stabilizer / Deconvolution & Batch Express / Hot Pixel Remover / Twin-Slicer / Ortho-Slicer / MIP-Renderer / PSF Renderer  / PSF distillerChromatic Aberration Corrector / Performance Option

Zeiss Zen 2.3

  • installation:
    • lite versions on all workstations
    • Zen 2.3 full version for stitching: workstations 2, 3, 4 and 5, additional Airyscan processing module on workstations 3 and 5

FlowJo connection

The leading platform for single-cell flow cytometry analysis that helps your research stand out.