Difference between revisions of "Informatics"

Revision as of 13:32, 16 October 2019

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

Software in use at pathology departments

Biobanking management

Centraxx.

Image analysis

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

Pathology wikis

Main article: 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.

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)

There is a push for an open virtual slide format.
A free C library exists to read whole-slide images.^[7]

Health informatics directory

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

References

↑ URL: http://www.cytomine.be/. Accessed on: 20 April 2016.
↑ 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.
↑ 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.
↑ 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/.
↑ 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.
↑ 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.
↑ URL: http://openslide.org/. Accessed on: 3 May 2013.
↑ URL: [http://hiww.org/ca.html http://hiww.org/ca.html]. Accessed on: November 8, 2014.

External links

Association of Pathology Informatics (pathologyinformatics.org).

[1] URL: http://www.cytomine.be/. Accessed on: 20 April 2016.

[pmid26755625-2] 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.

[pmid21282098-3] 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.

[pmid15563662-4] 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/.

[pmid17249408-5] 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] URL: http://openslide.org/. Accessed on: 3 May 2013.

[8] URL: [http://hiww.org/ca.html http://hiww.org/ca.html]. Accessed on: November 8, 2014.

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@@ Line 36: / Line 36: @@
 [https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal  | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref>
+[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.
 ==Whole-Slide Images==

Difference between revisions of "Informatics"

Revision as of 13:32, 16 October 2019

Contents

Software in use at pathology departments

Information systems

Dictation

Content management