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Image processing and analysis

 

The Platform provides help and assistance to users for image processing, analysis, quantification and interpretation.

Available software:

Imaris (Bitplane) : software for reconstruction and representation of 3-4-5 D images, and for image quantification and manipulation; it is interfaced with :

Fiji :

and Matlab : Mathworks Website: www.mathworks.fr

User manual

Amira (FEI): software for reconstruction and representation of 3-4-5 D images, and for image quantification and manipulation.

Website FEI: www.fei.com/software/amira-3d-for-life-sciences.

Matlab (MathWorks): Digital calculation programming software allowing the development of advanced processing (image processing, signal processing, statistics, etc.) on images. It can be interfaced with the software Imaris.

Website Mathworks: www.mathworks.fr

Huygens Pro (SVI – Scientific Volume Imaging): image deconvolution software; it allows the deflowering and denoising of images based on the knowledge of the physical and optical characteristics of the microscopes and the sample.

Website SVI: www.svi.nl

ImageJ et Fiji: free software for processing and analysing 3-4-5 D images with numerous plugins and allowing the creation of custom scripts (macros).

Icy:  Free software for processing and analysing 3-4-5 D images with many plugins and allowing the creation of custom scripts (macros).

Website: icy.bioimageanalysis.org

CellProfiler: free software for the quantification of large image series.

Website : www.cellprofiler.org

Zen (Zeiss): image manipulation software allowing the opening of images with the same interface as with the acquisition software of Zeiss microscopes; it also allows image analysis

Website Zen desk (Zeiss): www.zeiss.com/zen

Website Zen lite (Zeiss): www.zeiss.com/zen-lite

Metamorph Offline (Molecular Devices): image manipulation software allowing the opening of images with the same interface as with the Metamorph acquisition software; it also allows image analysis.

Website Metamorph: www.moleculardevices.com/products/software/meta-imaging-series/metamorph.html

Workstations

The software is installed on 2 powerful workstations.

  • Station 1 Imaris
    Processeur :
  • Station 3 Imaris
    Double processeur : 3,47 GHz, 12 cœurs physiques ; mémoire : 144 Go ; carte graphique : 6 Go.

A graphics tablet is also available, facilitating manual image segmentation operations.

User manual: