Difference between revisions of "Informatics"

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[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://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>


==Whole-Slide Images==
[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.
*Most common formats:
 
    **Philips (.tiff)
[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.
    **Aperio (.svs, .tif)
 
    **Hamamatsu (.vms, .vmu, .ndpi)
[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>
    **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.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref>


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