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Software in use at pathology departments

Information systems


Content management

Biobanking management

  • Centraxx.

Image analysis

  • Cytomine - under an Apache license.[1][2]

Pathology wikis

  • Wiki use for the dissemination of pathology knowledge is increasing.
  • In the general sphere, Wikipedia is dominating and will probably continue to do so.[3]

Open source

Open source in pathology appears to be some way off. One opinion paper[4] addresses this issue.

The radiologists are more on the ball here, e.g. UCLA's OpenSourcePACS.[5]

A few institutions (mostly American) are coming to understand this and have formed the Open Digital Pathology Consortium ( There is also an open slide project (

QPath is a open source software platform for whole slide image analysis.[6]

Cytomine is a web-based open source image processing and analysis software.

ASAP is an open-source whole-slide image viewer.

Ilastik - interactive learning and segmentation toolkit is an open source tool to perform segmentation and classification of images. Currently it does not support full virtual slides.[7]

Health informatics directory

  • The University of Freiburg put together a list in 2010.[8]

See also


  1. URL: Accessed on: 20 April 2016.
  2. Marée, R.; Rollus, L.; Stévens, B.; Hoyoux, R.; Louppe, G.; Vandaele, R.; Begon, JM.; Kainz, P. et al. (Jan 2016). "Collaborative analysis of multi-gigapixel imaging data using Cytomine.". Bioinformatics. doi:10.1093/bioinformatics/btw013. PMID 26755625.
  3. Heilman, JM.; Kemmann, E.; Bonert, M.; Chatterjee, A.; Ragar, B.; Beards, GM.; Iberri, DJ.; Harvey, M. et al. (2011). "Wikipedia: a key tool for global public health promotion.". J Med Internet Res 13 (1): e14. doi:10.2196/jmir.1589. PMID 21282098.
  4. Rubin A (December 2004). "An open pathology computer system". J. Clin. Pathol. 57 (12): 1252–3. doi:10.1136/jcp.2004.020826. PMC 1770514. PMID 15563662. //
  5. Bui, AA.; Morioka, C.; Dionisio, JD.; Johnson, DB.; Sinha, U.; Ardekani, S.; Taira, RK.; Aberle, DR. et al. (Jan 2007). "OpenSourcePACS: an extensible infrastructure for medical image management.". IEEE Trans Inf Technol Biomed 11 (1): 94-109. PMID 17249408.
  6. Bankhead, P.; Loughrey, MB.; Fernández, JA.; Dombrowski, Y.; McArt, DG.; Dunne, PD.; McQuaid, S.; Gray, RT. et al. (12 2017). "QuPath: Open source software for digital pathology image analysis.". Sci Rep 7 (1): 16878. doi:10.1038/s41598-017-17204-5. PMID 29203879.
  7. Berg, S.; Kutra, D.; Kroeger, T.; Straehle, CN.; Kausler, BX.; Haubold, C.; Schiegg, M.; Ales, J. et al. (Sep 2019). "ilastik: interactive machine learning for (bio)image analysis.". Nat Methods. doi:10.1038/s41592-019-0582-9. PMID 31570887.
  8. URL: []. Accessed on: November 8, 2014.

External links