Difference between revisions of "Digital pathology"

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*Typical cytology slide ~ 5 GB.
*Typical cytology slide ~ 5 GB.
*Typical anatomical pathology slide > 2 GB.
*Typical anatomical pathology slide > 2 GB.
==Whole-Slide Images==
*Most common formats:
    Aperio (.svs, .tif)
    Philips (.tiff)
    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.
* Most important criterion for virtual microscopy: Pathologists need the ability to rapidly pan and zoom images. When Z‑planes are available, viewers must also provide rapid scrolling though the planes.


==See also==
==See also==

Latest revision as of 14:05, 16 October 2019

Digital pathology is pathology done with a digital computer.

Digital slides

  • Typical cytology slide ~ 5 GB.
  • Typical anatomical pathology slide > 2 GB.

Whole-Slide Images

  • Most common formats:
   Aperio (.svs, .tif)
   Philips (.tiff)
   Hamamatsu (.vms, .vmu, .ndpi)
   Leica (.scn)
   Sakura (.svslide)
   MIRAX (.mrxs)
   Ventana (.bif, .tif)
   Generic tiled TIFF (.tif)

SlideJ is a plugin for ImageJ for viewing most of the above mentioned formats.[1] A free C library exists to read whole-slide images.[2]

  • There is a push for an open virtual slide format.
  • There is now a DICOM standard for whole slide images.
  • Most important criterion for virtual microscopy: Pathologists need the ability to rapidly pan and zoom images. When Z‑planes are available, viewers must also provide rapid scrolling though the planes.

See also

External links

  1. Della Mea, V.; Baroni, GL.; Pilutti, D.; Di Loreto, C. (2017). "SlideJ: An ImageJ plugin for automated processing of whole slide images.". PLoS One 12 (7): e0180540. doi:10.1371/journal.pone.0180540. PMID 28683129.
  2. URL: http://openslide.org/. Accessed on: 3 May 2013.