Image analysis software

The Imaging and Optics Facility provides various types of software for analysis of data acquired on our systems. The software can be used on our workstations based on their specifications. We aim to keep all the software up to date and in line with current trends in image analysis. If you need assistance with your image analysis or are missing some software you think is crucial please contact us

Bookable software for image analysis

Following software is licensed at IST and must be booked prior to use. Please follow the booking guidelines for each software and avoid blocking the licenses for other users.

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

Bitplane Imaris & Stitcher
3D/4D visualization and analysis software equipped with smart cell based segmentation and analysis tools tailored for use in biological research. Analysis includes automated tracking, detection of cell division and creation of interactive lineage trees along with statistical tests and a two-way interface for customization in Matlab, Java or Python as well as bridge to/from Fiji.

We have 8 x Imaris 9.3 floating licenses available on all our workstations. In case you booked a license and you cannot use it, this tool helps you to identify which user is using it without booking.

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

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


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

Kaluza software
 Simple and efficient tool for flow cytometry data analysis from Beckman Coulter.

SVI Huygens
 Software dedicated to enhancing microscopic images by deconvolution (Restoration to recover an image that is degraded by a physical process which can be described by the opposite operation, a convolution) and for chromatic aberration correction and other advanced image manipulations.

  • weblink:
  • installation: all workstations (2x floating license, book it as ‘equipment’ in addition to your workstation reservation!)
  • starter guide: TUTORIALS

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 distiller /  Chromatic Aberration Corrector / Performance Option

Zeiss Zen 2.3

Freeware for image and data analysis


Software package for analyzing, processing and visualizing multi-dimensional microscopy images

 A tool for storing, visualization, organization and analysis of images in the cloud.

Cell Profiler
Cell Profiler is a simple tool for semi-automated analysis and quantification of microscopic images. By using pipelines, object identification, classification and simple analysis (counting/measuring/..) of large amount of data providing simple output for quantification.

FIJI - ImageJ
Fiji is an image processing package: a “batteries-included” distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. On our workstation you can find FIJI equipped with the most commonly used and handy plugins.

Flowing software
Freeware tool for analysis of cytometry data designed for batch analysis by Cell Imaging Core of the Turku Centre for Biotechnology.

ICY is an open community platform for bioimage informatics (visualization, annotation and quantification) created by BioImage Analysis Lab at Institut Pasteur. 

A simple, user-friendly tool for interactive machine learning (ML) based image classification, segmentation and analysis.

Platform providing intuitive node-based workflow scheduler and data analysis tool.

Plant image analysis web
A database of image analysis tools, plug-ins and programs, mostly designed specifically for plant-related research

Commercial Freeware