Software

Unique solution for flow analysis and advanced data analysis. Compatible with all cytometer data files.

• Available at MRI-IGMM (dongle) and at l’IGH
• https://www.flowjo.com/solutions/flowjo

 Flowing Software is a free flow cytometry data analysis software for Windows. The project combines high throughput data analysis with flowing usability. The easy-to-use visual interface ensures an effective data analysis with your personal computer!

• Available at IGH
• http://flowingsoftware.btk.fi/

Harmony allows the offline-analysis of images coming from the opera automated microscope. Designed for biologists, Harmony’s workflow-based interface makes the whole process of high-content analysis straightforward, even for new users with little microscopy or programming knowledge.

See Harmony High-Content Imaging and Analysis Software

Software for analyzing images from automated plate acquisition systems. Allows dynamic measurements at cell, field and well level.

• Available at MRI-CRBM
• https://www.thermofisher.com/fr/fr/home/life-science/cell-analysis/cellular-imaging/high-content-screening/high-content-screening-instruments/hcs-studio-2.html

Image deconvolution, visualization and analysis software.

•  Available on all our workstations, via a floating licence server
• www.svi.nl

2D et 3D image processing and analysis software. Build on plugins, icy also provides the possibility to create ones own analysis protocols using visual programming. Scripts can be written in python and javascript.

• Available (on demand) on all workstations of the facility.
• http://icy.bioimageanalysis.org/

ILASTIK is an easy to use, open source, machine learning software. Different machine learning modules for segmentation (pixel classification), object classification and counting are available

• Available at MRI-CRBM et IGH
• https://www.ilastik.org/

3D image reconstruction and 3 and 4D image analysis software. Imaris consists of common modules like the surface rendering and the tracking and of specific modules with a limited number of available licenses like ImarisXT, Filament tracer or Cell. Imaris can interact with FIJI and via the XT module with matlab and python.

• Available on all workstations of the facility via the floating licence server
• www.bitplane.com

STED analysis software. Allows to visualize and manipulate multidimensional ABBERIOR images.

• Available on demand at MRI-IGH
• https://imspector.abberior-instruments.com/

The tool calculates the ratio of the intensity in the nuclei and the cytoplasm. It needs two images as input: the cytoplasm channel and the nuclei channel. The nuclei channel is used to segment the nuclei. The measurements are made in the cytoplasm channel after the background intensity has been corrected.

Download and further informations: Intensity Ratio Nuclei Cytoplasm Tool on github