Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations

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.

[1]  Carolina Wählby,et al.  In situ sequencing for RNA analysis in preserved tissue and cells , 2013, Nature Methods.

[2]  D. Rimm.  Next-gen immunohistochemistry , 2014, Nature Methods.

[3]  Pierre Geurts,et al.  Extremely randomized trees , 2006, Machine Learning.

[4]  R. Longuespée,et al.  Laser Microdissection-Based Microproteomics of Formalin-Fixed and Paraffin-Embedded (FFPE) Tissues. , 2018, Methods in molecular biology.

[5]  Oliver Rübel,et al.  OpenMSI: a high-performance web-based platform for mass spectrometry imaging. , 2013, Analytical chemistry.

[6]  J. Flanagan,et al.  RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. , 2012, The Journal of molecular diagnostics : JMD.

[7]  Marie-France Robbe,et al.  imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data. , 2012, Journal of proteomics.

[8]  Gilles Louppe,et al.  A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning , 2014, 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI).

[9]  Marc Niethammer,et al.  The power of correlative microscopy: multi-modal, multi-scale, multi-dimensional. , 2011, Current opinion in structural biology.

[10]  A. Koloydenko,et al.  Diagnosis of tumors during tissue-conserving surgery with integrated autofluorescence and Raman scattering microscopy , 2013, Proceedings of the National Academy of Sciences.

[11]  Richard M. Caprioli,et al.  Fusion of mass spectrometry and microscopy: a multi-modality paradigm for molecular tissue mapping , 2015, Nature Methods.

[12]  Mahadev Satyanarayanan,et al.  OpenSlide: A vendor-neutral software foundation for digital pathology , 2013, Journal of pathology informatics.

[13]  Edmund Koch,et al.  Assessing the efficacy of coherent anti‐Stokes Raman scattering microscopy for the detection of infiltrating glioblastoma in fresh brain samples , 2017, Journal of biophotonics.

[14]  Mark Kriegsmann,et al.  MALDI mass spectrometry imaging: A cutting‐edge tool for fundamental and clinical histopathology , 2016, Proteomics. Clinical applications.

[15]  Zoltan Takats,et al.  Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging. , 2010, Angewandte Chemie.

[16]  David C Muddiman,et al.  MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform , 2013, Journal of The American Society for Mass Spectrometry.

[17]  Mark Kriegsmann,et al.  A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing. , 2016, Methods.

[18]  Pierre Jeannesson,et al.  Fully unsupervised inter‐individual IR spectral histology of paraffinized tissue sections of normal colon , 2016, Journal of biophotonics.

[19]  M. Askenazi,et al.  The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5 , 2016, Mass spectrometry reviews.

[20]  Andrew Zisserman,et al.  Microscopy cell counting and detection with fully convolutional regression networks , 2018, Comput. methods Biomech. Biomed. Eng. Imaging Vis..

[21]  Gilles Louppe,et al.  Collaborative analysis of multi-gigapixel imaging data using Cytomine , 2016, Bioinform..

[22]  Milad Nazari,et al.  MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses , 2017, Journal of The American Society for Mass Spectrometry.

[23]  J. Buhmann,et al.  Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry , 2014, Nature Methods.

[24]  R. Caprioli.  Imaging mass spectrometry: Molecular microscopy for the new age of biology and medicine , 2016, Proteomics.

[25]  Carolina Wählby,et al.  Next-generation pathology--surveillance of tumor microecology. , 2015, Journal of molecular biology.

[26]  Raphaël Marée,et al.  A machine learning approach for material detection in hyperspectral images , 2009, 2009 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops.

[27]  U. Landegren,et al.  Direct observation of individual endogenous protein complexes in situ by proximity ligation , 2006, Nature Methods.

[28]  Josephine Bunch,et al.  SpectralAnalysis: Software for the Masses. , 2016, Analytical chemistry.

[29]  Lucas Pelkmans,et al.  Image-based transcriptomics in thousands of single human cells at single-molecule resolution , 2013, Nature Methods.

[30]  C. Rueden,et al.  Metadata matters: access to image data in the real world , 2010, The Journal of cell biology.