Interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology

Chris Gorman, Davide Punzo, Igor Octaviano, Steven Pieper, William J. R. Longabaugh, David A. Clunie, Ron Kikinis, Andrey Y. Fedorov () and Markus D. Herrmann ()
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Chris Gorman: Massachusetts General Hospital and Harvard Medical School
Davide Punzo: Radical Imaging
Igor Octaviano: Radical Imaging
Steven Pieper: Isomics Inc
William J. R. Longabaugh: Institute for Systems Biology
David A. Clunie: PixelMed Publishing LLC
Ron Kikinis: Brigham and Women’s Hospital and Harvard Medical School
Andrey Y. Fedorov: Brigham and Women’s Hospital and Harvard Medical School
Markus D. Herrmann: Massachusetts General Hospital and Harvard Medical School

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and interoperability, which is detrimental to the reproducibility of scientific findings and clinical integration of technological innovations. We introduce Slim, an open-source, web-based slide microscopy viewer that implements the internationally accepted Digital Imaging and Communications in Medicine (DICOM) standard to achieve interoperability with a multitude of existing medical imaging systems. We showcase the capabilities of Slim as the slide microscopy viewer of the NCI Imaging Data Commons and demonstrate how the viewer enables interactive visualization of traditional brightfield microscopy and highly-multiplexed immunofluorescence microscopy images from The Cancer Genome Atlas and Human Tissue Atlas Network, respectively, using standard DICOMweb services. We further show how Slim enables the collection of standardized image annotations for the development or validation of machine learning models and the visual interpretation of model inference results in the form of segmentation masks, spatial heat maps, or image-derived measurements.

Date: 2023
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DOI: 10.1038/s41467-023-37224-2

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