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Diagnostic Pathology

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Open Access 01-12-2013 | Software

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

Authors: Matloob Khushi, Georgina Edwards, Diego Alonso de Marcos, Jane E Carpenter, J Dinny Graham, Christine L Clarke

Published in: Diagnostic Pathology | Issue 1/2013

Abstract

Background

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 (http://www.abctb.org.au) 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. NDPI-Splitter also has the capacity to filter out empty images.

Conclusions

Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis.

Virtual Slides

The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5330903258483934

Available only for authorised users

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Title: Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information
Authors: Matloob Khushi
Georgina Edwards
Diego Alonso de Marcos
Jane E Carpenter
J Dinny Graham
Christine L Clarke
Publication date: 01-12-2013
Publisher: BioMed Central
Published in: Diagnostic Pathology / Issue 1/2013
Electronic ISSN: 1746-1596
DOI: https://doi.org/10.1186/1746-1596-8-22

Keynote webinar | Spotlight on medication adherence

Springer Medicine

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

Abstract

Background

Results

Conclusions

Virtual Slides

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Background

Results

Conclusions

Virtual Slides

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