Tissue section听digitalization has opened the way to automation of image analyzes.
2IP proposes a support for image analysis on the following software:
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2D scans听
鈻禾� 听听QuPath听
free open source software, easy to use
compatible with .scn,听.czi and .mrxs formats
compatible with听brightfield, fluorescence (max 3 colors for .mrxs files) and polarized light scans
application examples: PSR stained area, cell counting,...
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听(in French)
more infos听and on Pete Bankhead Youtube chain
Please cite this article in your publications:听Bankhead, P. et al. (2017). QuPath: Open source software for digital pathology image analysis. Scientific Reports.
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鈻禾� 听 Author (Visiopharm)听听
2 licences available locally at 2IP
compatible with .scn, .czi, .mrxs formats
compatible with听brightfield, fluorescence (including multiplex) and polarized light scans
multiple scan听alignment possible
application examples:听 听 听tumor infiltrating immune cells
fibrosis regional density
cell hypertrophy...
鈻禾� 听Halo (Indica Labs)听 听 听听
1 licence听available locally at 2IP (+ 2 licences available at DDUV)
compatible with .scn, .czi, .mrxs formats
compatible with听brightfield, fluorescence (including multiplex) and polarized light scans
multiple scan听alignment听possible
artificial intelligence
application examples:听 tumor infiltrating immune cells, ...
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Images (.tiff preferably)
鈻� ImageJ/Fiji听
ImageJ is a free software based on JAVA language, developed by the NIH and broadly used by the scientific community. Numerous plugins and macros are available and allow to perform custom operations.
Link to download听听or听
application examples:听 听 听cell counting
collagen fibers density (PSR in polarized light)
distance between lysosomes and nucleus
鈻禾齔EN blue听
1 licence听available locally at 2IP
colocalization, dynamic, spectral unmixing, FRET, FRAP modules
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鈻� QuPath听
see above
鈻� Author (Visiopharm)听
see above
鈻� Halo (Indica Labs)听
see above
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3D scans
鈻� Imaris听(Bitplane)听
1 licence听available locally at 2IP
useful tutorials:听
鈻� Vision4D (Arivis)听
听 听 听 听 听听 听听 听 听 听 听 听 听 听听 听 1 licence听available locally at 2IP听 听 听 听 听听 听 听 听 听听 听 听 听 听 听 听
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