Informatics

From Libre Pathology
Revision as of 13:38, 16 October 2019 by Jensflorian (talk | contribs) (→‎Whole-Slide Images: SlideJ for ImageJ)
Jump to navigation Jump to search

Informatics is the management of information. Pathologists, unfortunately, mostly have poor tools for this job.

Software in use at pathology departments

Information systems

Dictation

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 (opendp.org). There is also an open slide project (openslide.org).

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.

Whole-Slide Images

  • Most common formats:
   **Philips (.tiff)
   **Aperio (.svs, .tif)
   **Hamamatsu (.vms, .vmu, .ndpi)
   **Leica (.scn)
   **Sakura (.svslide)
   **MIRAX (.mrxs)
   **Ventana (.bif, .tif)
   **Generic tiled TIFF (.tif)

SlideJ is a plugin for ImageJ for viewing most of the above mentioned formats.[7]

  • There is a push for an open virtual slide format.
  • A free C library exists to read whole-slide images.[8]

Health informatics directory

  • The University of Freiburg put together a list in 2010.[9]

See also

References

  1. URL: http://www.cytomine.be/. 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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1770514/.
  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. Della Mea, V.; Baroni, GL.; Pilutti, D.; Di Loreto, C. (2017). "SlideJ: An ImageJ plugin for automated processing of whole slide images.". PLoS One 12 (7): e0180540. doi:10.1371/journal.pone.0180540. PMID 28683129.
  8. URL: http://openslide.org/. Accessed on: 3 May 2013.
  9. URL: [http://hiww.org/ca.html http://hiww.org/ca.html]. Accessed on: November 8, 2014.

External links