Other Software

The following software are also available from our image processing workstations.

CellProfiler is free, open-source software for quantitative analysis of biological images. No prior experience in programming or computer vision is required.

QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.

Ilastik is a versatile software, originally 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).

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

Zeiss Zen (black and blue) to work offline on the data acquired from Zeiss microscopes.

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 a fluorescent image stack (mouse embryo, acquired with MacroSPIM) together with the extracted embryo isosurface (Imaris)

Same embryo visualized with different blending settings for isosurface + 1 cutting plane (Imaris + ImageJ)

From the same embryo, visualized organs close ups, with isosurface cutting plane. Segmentation of organs: Ilastik, (Imaris + ImageJ)

Nuclei counting and 3D rendering. Imaris 3D rendering (MIP) + detected nuclei

Stained blood vessels 3D stack (MacroSPIM) Imaris rendering (Shadow projection)

Blood vessels 3D stack , skeleton

Nucleus tracking in 3D+t data set.

(Image courtesy of Sylvia Ruth Dyballa, Universidad Pompeu Fabra)

Check this project