TissueMaps: A large multi-scale data analysis platform for digital image application built on open-source software
2016 (English)Conference paper, Poster (Other academic)
Automated analysis of microscopy data and quantification of cell and tissue morphology has become an important tool for investigating disease and/or drug response. New methods of in situ sequencing of RNA allows profiling of gene expression at cellular resolution in intact tissue samples, and thus opens up for large-scale comparison of genotype and phenotype. Expressed genes are locally amplified by molecular probes and rolling circle amplification, and decoded by analysis of repeated imaging and sequencing cycles. Using image processing methodologies on these giga-pixel images (40000 x 48000 pixels), we have identified more than 40 genes in parallel in the same tissue sample. On the other hand, the distribution and organisation of cells in the tissue contain rich information at multiple resolutions. The lowest resolution describes the global tissue arrangement, while the cellular resolution allows us to quantify gene expression and morphology of individual cells.
Here, we present an open-source tool which combine the analysis of gene expression with quantification of cell and tissue morphology. Our framework builds on CellProfiler, a free and open-source software developed for image based screening, and our viewing platform allow experts to visualize analysis results with different overlays, such as the commonly used H&E staining. Furthermore, the user can draw regions of interest and extract local statistics on gene expression and tissue morphology over large slide scanner images at different resolutions (Fig.1). The TissueMaps platform provides a flexible solution to support the future development of histopathology, both as a diagnostic tool and as a research field.
Place, publisher, year, edition, pages
Medical Image Processing
Research subject Computerized Image Processing
IdentifiersURN: urn:nbn:se:uu:diva-309621OAI: oai:DiVA.org:uu-309621DiVA: diva2:1052336
4th Nordic Symposium on Digital Pathology