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Informatics (view source)

Revision as of 14:00, 16 October 2019

1,037 bytes removed ,  14:00, 16 October 2019
Update on open source and move of slide section to digital pathology
(→‎Whole-Slide Images: DICOM standard)
(Update on open source and move of slide section to digital pathology)
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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==
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