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 :
- Website ImageJ: http://imagej.nih.gov/ij
- Website Fiji: http://fiji.sc/Fiji
- Wiki on ImageJ and Fiji: http://imagejdocu.tudor.lu
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).
- Website ImageJ: http://imagej.nih.gov/ij
- Website Fiji: http://fiji.sc/Fiji
- Wiki on ImageJ and Fiji: http://imagejdocu.tudor.lu
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:
