Other Software

The following software are available in our image processing workstations.


Ilastik is a versatile software based on the optimized C++ image processing library VIGRA. It implements a multiple class segmentation based on fast and interactive pixel based classification (2D/3D). In the learning phase the user "paints" the objects with different color depending on their type and the selection can be iteratively refined. The software also implements an efficient seeded carving algorithm to extract complex 3D shapes in a 3D stack, possible applications are neuron segmentation in EM stacks or organ extraction in embryo images.     


Imaris is Bitplane’s core scientific software for 3D data visualization, processing, rendering, analysis, segmentation, tracking and interpretation of 3-,4- and 5-D datasets. We use it mainly for visualization of 3D data sets where it excels (original data set, processed data set or annotated data set). We also use it for simple 3D analysis when the images are well adapted and of sufficient quality (Isosurface extraction, nuclei counting, nuclei tracking). 

Available modules: ImarisMeasurement Pro, ImarisTrack, ImarisColoc, FilamentTracer, ImarisVantage, Imaris InPress.

LAS AF (Leica Application Suite AF)

LAS is developed by Leica Microsystems CMS GmbH to work offline on the data acquired from Leica microscopy systems. 

Available modules: LAS AF Base License, 3D Visualization, Colocalization, Dye Finder, Motion Spy.

Igor Pro 6

Igor pro can be used for statistical analysis, numeric data management (like Excel but targeted to scientific data analysis), curve fitting, advanced graphing & plotting.

Example Applications


3D rendering (blend) of the original                 Same as left figure with different
stack (mouse embryo acquired with                blending settings + cutting plane
MacroSPIM) together with the               
extracted embryo isosurface (extraction 
+ visualization performed in Imaris)

Extraction of different organs performed with Ilastik    Nuclei counting and 3D rendering (MIP) 
Imaris 3D rendering + overlay with original dataset                    performed in Imaris

Stained blood vessels 3D stack (MacroSPIM)                           Same as left figure, skeleton extracted by
Imaris rendering (Shadow projection)                           ImageJ macro (see this page), Imaris rendering (blend)

    Nucleus tracking in 3D+t data set. Tracking and visualization performed in Imaris
        (Image courtesy of Sylvia Ruth Dyballa, Universidad Pompeu Fabra)
                                                Download video