Difference between revisions of "Informatics"

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(→‎Whole-Slide Images: DICOM standard)
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[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Cureently 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>
[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Cureently 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>
==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)
[https://imagej.net/SlideJ SlideJ] is a plugin for ImageJ for viewing most of the above mentioned formats.<ref>{{Cite journal  | last1 = Della Mea | first1 = V. | last2 = Baroni | first2 = GL. | last3 = Pilutti | first3 = D. | last4 = Di Loreto | first4 = C. | title = SlideJ: An ImageJ plugin for automated processing of whole slide images. | journal = PLoS One | volume = 12 | issue = 7 | pages = e0180540 | month =  | year = 2017 | doi = 10.1371/journal.pone.0180540 | PMID = 28683129 }}</ref> A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref>
*There is a push for an open virtual slide format.
*There is now a [http://dicom.nema.org/Dicom/DICOMWSI/ DICOM] standard for whole slide images.


==Health informatics directory==
==Health informatics directory==

Revision as of 14:00, 16 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. Cureently 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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