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Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations
Author(s) -
Rubens Ulysse,
Hoyoux Renaud,
Vanosmael Laurent,
Ouras Mehdy,
Tasset Maxime,
Hamilton Christopher,
Longuespée Rémi,
Marée Raphaël
Publication year - 2019
Publication title -
proteomics – clinical applications
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.948
H-Index - 54
eISSN - 1862-8354
pISSN - 1862-8346
DOI - 10.1002/prca.201800057
Subject(s) - computer science , preprocessor , digital pathology , software , mass spectrometry imaging , maldi imaging , laser capture microdissection , proteomics , pathology , artificial intelligence , medicine , mass spectrometry , chemistry , matrix assisted laser desorption/ionization , biochemistry , gene expression , organic chemistry , chromatography , adsorption , desorption , gene , programming language
Purpose Digital histology is being increasingly used in research and clinical applications. In parallel, new tissue imaging methods (e.g., imaging mass spectrometry) are currently regarded as very promising approaches for better molecular diagnosis in pathology. However, these new data sources are still often underexploited because of the lack of collaborative software to share and correlate information for multimodal analysis. Experimental design The open science paradigm is followed to develop new features in the web‐based Cytomine software to support next‐generation digital pathology bridged to molecular investigations. Results New open‐source developments allow to explore whole‐slide classical histology with Matrix Assisted Laser Desorption Ionisation (MALDI) imaging and to support preprocessing for biomarker discovery using laser microdissection‐based microproteomics. Conclusions and clinical relevance The updated version of Cytomine is the first open and web‐based tool to enable sharing data from classical histology, molecular imaging, and cell counting for proteomics preprocessing. It holds good promise to fulfill imminent needs in molecular histopathology.