Difference between revisions of "Informatics"

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'''Informatics''' is the management of information.   
'''Informatics''' is the management of information. [[Pathologist]]s, unfortunately, mostly have poor tools for this job.   


Pathologists, unfortunately, only have abysmal tools for this job.
==Software in use at pathology departments==
===Information systems===
*[[Softpath]].
*[[CoPath]].
*[[MEDITECH]].
*[[Millennium]].
*Nexus pas.net.
*[[VANTAGE]].


The two main information systems (''[[Softpath]]'' and ''[[CoPath]]'') are pathetic and look like they are out of the early 1990s.
===Dictation===
*[[Dragon]].
*[[Voicebrook]].
 
===Content management===
*[[Paradigm]].
 
===Biobanking management===
* Centraxx.
 
===Image analysis===
* Cytomine - under an  ''Apache license''.<ref>URL: [http://www.cytomine.be/ http://www.cytomine.be/]. Accessed on: 20 April 2016.</ref><ref name=pmid26755625>{{Cite journal  | last1 = Marée | first1 = R. | last2 = Rollus | first2 = L. | last3 = Stévens | first3 = B. | last4 = Hoyoux | first4 = R. | last5 = Louppe | first5 = G. | last6 = Vandaele | first6 = R. | last7 = Begon | first7 = JM. | last8 = Kainz | first8 = P. | last9 = Geurts | first9 = P. | title = Collaborative analysis of multi-gigapixel imaging data using Cytomine. | journal = Bioinformatics | volume =  | issue =  | pages =  | month = Jan | year = 2016 | doi = 10.1093/bioinformatics/btw013 | PMID = 26755625 }}</ref>
 
==Pathology wikis==
{{Main|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.<ref name=pmid21282098>{{Cite journal  | last1 = Heilman | first1 = JM. | last2 = Kemmann | first2 = E. | last3 = Bonert | first3 = M. | last4 = Chatterjee | first4 = A. | last5 = Ragar | first5 = B. | last6 = Beards | first6 = GM. | last7 = Iberri | first7 = DJ. | last8 = Harvey | first8 = M. | last9 = Thomas | first9 = B. | title = Wikipedia: a key tool for global public health promotion. | journal = J Med Internet Res | volume = 13 | issue = 1 | pages = e14 | month =  | year = 2011 | doi = 10.2196/jmir.1589 | PMID = 21282098 }}</ref>


==Open source==
==Open source==
Open source in pathology appears to be a long way off.  One paper,<ref name=pmid15563662>{{cite journal |author=Rubin A |title=An open pathology computer system |journal=J. Clin. Pathol. |volume=57 |issue=12 |pages=1252–3 |year=2004 |month=December |pmid=15563662 |pmc=1770514 |doi=10.1136/jcp.2004.020826 |url=}}</ref> gives me a bit of hope -- though I think this is a voice in the wilderness.   
Open source in pathology appears to be some way off.  One opinion paper<ref name=pmid15563662>{{cite journal |author=Rubin A |title=An open pathology computer system |journal=J. Clin. Pathol. |volume=57 |issue=12 |pages=1252–3 |year=2004 |month=December |pmid=15563662 |pmc=1770514 |doi=10.1136/jcp.2004.020826 |url=}}</ref> addresses this issue. 
 
The radiologists are more on the ball here, e.g. [http://www.mii.ucla.edu/opensourcepacs-download-2/ UCLA's OpenSourcePACS].<ref name=pmid17249408>{{Cite journal  | last1 = Bui | first1 = AA. | last2 = Morioka | first2 = C. | last3 = Dionisio | first3 = JD. | last4 = Johnson | first4 = DB. | last5 = Sinha | first5 = U. | last6 = Ardekani | first6 = S. | last7 = Taira | first7 = RK. | last8 = Aberle | first8 = DR. | last9 = El-Saden | first9 = S. | title = OpenSourcePACS: an extensible infrastructure for medical image management. | journal = IEEE Trans Inf Technol Biomed | volume = 11 | issue = 1 | pages = 94-109 | month = Jan | year = 2007 | doi =  | PMID = 17249408 }}</ref> 
 
A few institutions (mostly American) are coming to understand this and have formed the [http://www.opendp.org/ Open Digital Pathology Consortium (opendp.org)]. There is also an [http://openslide.org/ open slide project (openslide.org)].
 
[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.
 
[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.
 
[https://www.ilastik.org/ 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.<ref>{{Cite journal  | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume =  | issue = | pages =  | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref>


[[IMHO]], most pathologists understand very little about computers and those that think they know something often know precious little.
==Health informatics directory==
*The University of Freiburg put together a list in 2010.<ref>URL: [http://hiww.org/ca.html
http://hiww.org/ca.html]. Accessed on: November 8, 2014.</ref>
 
==See also==
*[[Quality]].
*[[Digital pathology]].
*[[Journal of Pathology Informatics]].


==References==
==References==
{{reflist|1}}
{{reflist|2}}
 
==External links==
*[http://pathologyinformatics.org/ Association of Pathology Informatics (pathologyinformatics.org)].


[[Category:Informatics]]
[[Category:Informatics]]

Latest revision as of 09:34, 18 October 2019

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

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.

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

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

External links

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