Image analysis softwares

BioVis offers you free access to several image analysis softwares. We run introductory courses on image analysis softwares on a regular basis and can help you get started with your analysis. 

Image of Huygens


Deconvolution improves the quality of images, resolution and noise, based on the known optical properties of the microscope and fluorophores – unlike Photoshop. The gain can be substantial, especially for widefield images when the out of focus blur is removed. Deconvolution also substantially improves confocal and multiphoton images.

For more information about the Huygens software please contact


Image analysis allows you to extract numerical data from your images. Image reconstruction simplifies vast amounts of visual information found in 3- and 4-D data sets. Image processing allows you to enhance the quality of the image.

The IMARIS software allows you to identify, render and segment 3D-, filamentous- and point-like structures including their change and tracks over time (4D), also tracking the fate of dividing cells.

Identifications and segmentations of such structures can be done automatically or manually and even edited, sorted, grouped, exported and used for batch analysis.

IMARIS will guide you through each analysis feature over the wizard tool where certain important parameter like threshold and filters can be managed. Settings used can be stored to be reviewed, refined or used in Batch applications. Statistical data like volume, surface, speed, intensities, angles and many more are calculated ad hoc for you, just choose from the vast amount of available numerical data calculated in IMARIS.

Analyse your multi-channel data set for Colocalization and even create new channels by using surfaces you created as masks. Last but not least present your data, as snapshots or a movie, guiding the viewer through your analysis and re-construction. Getting to know the software is an easy task thanks to its user-friendly interface, a homepage and Youtube channel filled with valuable information for the beginner to the advanced user.

For more information about IMARIS please contact

Imaris modules
  • Core
  • Measurement Pro
  • Filament Tracer
  • Track
  • Batch
  • Colocalization

Cell Profiler

Cell Profiler is a free open source software it is ideal for automatically analysing 2D images of cells. You can upload single images or large datasets with multiple fluorophores. The analysis is created from menus and can be stored, reused and shared.
Our collaboration partners at the Centre for image analysis can help you if you have any further questions.

For more information visit the Cellprofiler web site.

Image J and Fiji

ImageJ and Fiji are open source image processing programs designed for scientific multidimensional images. They are highly extensible, with thousands of plugins and scripts for performing a wide variety of tasks, and a large user community.

If you want to learn more about Image J and Fiji  BioVis offers several courses please contact for more information.