Open Source Tools For Management And Archiving Of Digital Microscopy Data To Allow Integration With Patient Pathology And Treatment Information

Matloob Khushi, Georgina Edwards, Diego Alonso de Marcos, Jane E Carpenter, J Dinny Graham, Christine L Clarke | 7th Space Interactive | February 12, 2013

Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. Results: We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter.

Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patient's clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website ( using Deep Zoom open source technology.

Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab...