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Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information

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Document pages: 7 pages

Abstract: Virtual microscopy includes digitisation of histology slides and the use ofcomputer technologies for complex investigation of diseases such as cancer.However, automated image analysis, or website publishing of such digitalimages, is hampered by their large file sizes. We have developed two Java basedopen source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creatorconverts a portion of a large digital slide into a desired quality JPEG image.The image is linked to the patients clinical and treatment information in acustomised open source cancer data management software (Caisis) in use at theAustralian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTBwebsite this http URL using Deep Zoom open source technology. Using theABCTB online search engine, digital images can be searched by defining variouscriteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits alarge image file into smaller sections of TIFF images so that they can beeasily analysed by image analysis software such as Metamorph or Matlab.NDPI-Splitter also has the capacity to filter out empty images. SnapshotCreator and NDPI-Splitter are novel open source Java tools. They convertdigital slides into files of smaller size for further processing. Inconjunction with other open source tools such as Deep Zoom and Caisis, thissuite of tools is used for the management and archiving of digital microscopyimages, enabling digitised images to be explored and zoomed online. Our onlineimage repository also has the capacity to be used as a teaching resource. Thesetools also enable large files to be sectioned for image analysis.

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