Developed at the Research Center  "E. Piaggio", University of Pisa, the freeware (and few images we used to validate the tool) can  be downloaded at this link. The source code can be downloaded at this link.

HisTOOLogy is a user-friendly tool developed for the quantification of colour image of histological sections.



It includes:

  • An intuitive colour separation algorithm to accurately and reproducibly return the amount of colour per unit area, implemented for the most common histochemical stains (e.g. Haematoxylin-Eosin, Alcian Blue-PAS, Orcein and Masson's trichrome)
  • Friendly interactive graphical user interfaces, that enable both expert and non-expert users to extract colour information from stained samples.

HisTOOLogy is designed with an open architecture. This provides extensibility via Matlab scripts that can be implemented by users with programming knowledge for their own tasks.

For additional information, contact:  



C. Magliaro, A. Tirella, G. Mattei, A. Pirone, A. Ahluwalia, "HisTOOLogy: an open-source tool for quantitative analysis of histological sections", Journal of Microscopy, August 2015, DOI: 10.1111/jmi.12292.


HisTOOLogy is was developed thanks to funding from the EU (ReLiver-  

* Users are kindly asked to cite the paper and the software source.