Image analysis

2IP

Tissue section digitalization has opened the way to automation of image analyzes.

2IP proposes a support for image analysis on the following software:

 

  • 2D scans 

►    QuPath 

free open source software, easy to use

compatible with .scn and .czi formats (not .mrxs)

compatible with brightfield, fluorescence (max 3 colors) and polarized light scans

application examples: PSR stained area, cell counting,...

 

link to download

2IP short user guide (in French)

more infos here and on Pete Bankhead Youtube chain

Please cite this article in your publications: Bankhead, P. et al. (2017). QuPath: Open source software for digital pathology image analysis. Scientific Reports. https://doi.org/10.1038/s41598-017-17204-5

 

►    Author (Visiopharm)  

2 licences available locally at 2IP

compatible with .scn, .czi, .mrxs formats

compatible with brightfield, fluorescence (including multiplex) and polarized light scans

multiple scan alignment possible

application examples:     tumor infiltrating immune cells

fibrosis regional density

cell hypertrophy...

►   Halo (Indica Labs)      

1 licence available locally at 2IP (+ 2 licences available at DDUV)

compatible with .scn, .czi, .mrxs formats

compatible with brightfield, fluorescence (including multiplex) and polarized light scans

multiple scan alignment possible

artificial intelligence

application examples:  tumor infiltrating immune cells, ...

 


  • Images (.tiff preferably)

► ImageJ/Fiji 

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 ImageJ or Fiji

application examples:     cell counting

collagen fibers density (PSR in polarized light)

distance between lysosomes and nucleus

► ZEN blue 

1 licence available locally at 2IP

colocalization, dynamic, spectral unmixing, FRET, FRAP modules

 

► QuPath 

see above

► Author (Visiopharm) 

see above

► Halo (Indica Labs) 

see above

 


  • 3D scans

► Vision4D (Arivis) 

                               1 licence available locally at 2IP