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research:computer-aided-histopathology [2020/02/18 11:38] pkleczek [WSIs] |
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| - | ====== Computer-aided pathology ====== | ||
| - | Below I collected and summarized some useful resources on computer-aided pathology. | ||
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| - | ===== Stain normalization & stain unmixing (implementations) ===== | ||
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| - | * [[https://github.com/mitkovetta/staining-normalization|Mitko Veta's repo]], [[http://amida13.isi.uu.nl/?q=node/69|MICCAI 2013 Grand Challenge – Staining unmixing and normalization]] | ||
| - | * Macenko et al. | ||
| - | * [[https://www2.warwick.ac.uk/fac/sci/dcs/research/combi/research/bic/software/|BIA Lab - Software]] (Stain Normalisation Toolbox) | ||
| - | * RGB Histogram Specification, Reinhard et al., Macenko et al., Khan et al. | ||
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| - | ===== Datasets of histopathological images ===== | ||
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| - | ==== Study images ==== | ||
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| - | Images with descriptions by histopathologists -- a good starting point to get a better understanding of tissue biology. | ||
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| - | * [[http://www.histologyguide.org/slidebox/slidebox.html|Histology Guide]] (T. Clark Brelje, Robert L. Sorenson) | ||
| - | * Pathorama (University of Basel) | ||
| - | * [[http://pathorama.ch/vcollections/index.html|Pathorama - vCollections]] | ||
| - | * [[http://pathorama.ch/vslides/index.html|Pathorama - vSlides]] | ||
| - | * [[http://alf3.urz.unibas.ch/pathopic/e/intro.htm|Pathorama - PathoPic]] | ||
| - | * [[http://www.mbfbioscience.com/iowavirtualslidebox|The Iowa Virtual Slidebox]] (MBF Bioscience) \\ To browse images you need //Biolucida// software. | ||
| - | * [[http://missinglink.ucsf.edu/lm/ids_101_histo_resource/index.htm|Prologue Histology Resource]] (UCSF School of Medicine) \\ Within each laboratory you need to click the "//Labeled version//" links. | ||
| - | |||
| - | ==== WSIs ==== | ||
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| - | :!: Most repositories use ImageScope to manage slide collections (see [[research:computer-aided-histopathology:imagescope|ImageScope]] for more information). | ||
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| - | * **University of British Columbia:** [[http://histo.anat.ubc.ca/|VirtualSLIDEBOX]] | ||
| - | * dermopathology: [[http://histo.anat.ubc.ca/PATHOLOGY/Anatomical%20Pathology/DermPath/view.apml|DermPath]] | ||
| - | * **University of Leeds:** [[http://www.virtualpathology.leeds.ac.uk/slidelibrary/slidelibrary_advanced.php|Virtual Pathology Slide Library]] | ||
| - | * **Duke University:** [[http://vmw-aperioimg03.duhs.duke.edu/|Virtual Slide Collection]] \\ NOTE: Images are unsortod, searching not supported. | ||
| - | * **University of Michigan:** [[https://www.pathology.med.umich.edu/slides/index.php|Virtual Slide Box]] | ||
| - | * dermatopathology: [[https://www.pathology.med.umich.edu/slides/search.php?collection=Andea&dxview=show|Andrea]], <del>[[https://www.pathology.med.umich.edu/slides/search.php?collection=Arps&dxview=show|Arps]]</del>, [[https://www.pathology.med.umich.edu/slides/search.php?collection=AndeaTch&dxview=show|AndreaTch]], [[https://www.pathology.med.umich.edu/slides/search.php?collection=DermPath&dxview=show|DermPath]], <del>[[https://www.pathology.med.umich.edu/slides/search.php?collection=DermPathConf&dxview=show|DermPathConf]]</del>, [[https://www.pathology.med.umich.edu/slides/search.php?collection=Rajiv_Patel&dxview=show|Patel]] | ||
| - | * **(various universities):** [[http://virtualslides.med.umich.edu/|Slide Collection]] \\ Links to images grouped by the type of tissue: [[https://web.duke.edu/histology/SlideIndex.html|SlideIndex]] | ||
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| - | * **Digital Pathology Association:** [[https://digitalpathologyassociation.org/whole-slide-imaging-repository|Whole Slide Imaging Repository]] \\ Links to further web pages with atlases of pathological images (created by universities). | ||
| - | * [[https://wiki.cancerimagingarchive.net/display/Public/CPTAC-CM|CPTAC-CM]] | ||
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| - | |||
| - | ==== Histo(patho)logical atlases ==== | ||
| - | |||
| - | * [[http://www.anatomyatlases.org/MicroscopicAnatomy/MicroscopicAnatomy.shtml|Atlas of Microscopic Anatomy]] | ||
| - | * [[https://pl.wikibooks.org/wiki/Atlas_histopatologii_guz%C3%B3w_sk%C3%B3ry|Atlas histopatologii guzów skóry]] (Leszek Woźniak, Krzysztof W. Zieliński) | ||
| - | * [[http://melanocytepathology.com/slide-sets/|Melanocyte Pathology - Slide Sets]] \\ Cases of melanocytic lesions with exhaustive diagnoses and appropriate images. | ||
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| - | ===== Datasets ===== | ||
| - | |||
| - | (a.a. sets used for machine-learing tasks -- often contain //ground truth//) | ||
| - | |||
| - | * [[https://www2.warwick.ac.uk/fac/sci/dcs/research/combi/research/bic/data/|BIA Lab: Datasets for Sharing]] | ||
| - | * [[https://mitos-atypia-14.grand-challenge.org/dataset/|MITOS-ATYPIA-14 Challange]] (H&E-stained breast cancer, images taken under x20 and x40 magnification) | ||
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| - | ===== Online courses ===== | ||
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| - | ==== Histo(patho)logy ==== | ||
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| - | * **[[http://www.histology.leeds.ac.uk/index.php|The Histology Guide]]** -- University of Leeds \\ A good and accessible description of histological techniques. | ||
| - | * [[https://histologie.unibas.ch/index.php/info.html|Kurs histologii ogólnej]] (niem.) – Universität Basel, Medizinische Fakultät (2009) | ||
| - | * [[https://eliph.klinikum.uni-heidelberg.de/|Kurs patologii ogólnej]] (niem.) – Universitätsklinikum Heidelberg | ||
| - | * [[https://pathobasic.wordpress.com/|PathoBasic - Essential Pathology for Residents]] – within the Pathorama project | ||
| - | * [[http://cnx.org/contents/Fho-qM2D@1.1:tZedWrCQ@3/Histology-Module-1-Introductio|Histology]] – Rice University | ||
| - | * [[https://ocw.mit.edu/courses/health-sciences-and-technology/hst-035-principle-and-practice-of-human-pathology-spring-2003/index.htm|Principle and Practice of Human Pathology]] -- MIT | ||
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| - | ==== Anatomy ==== | ||
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| - | * [[http://cnx.org/contents/FPtK1zmh@8.25:zMTtFGyH@4/Introduction|Anatomy & Physiology]] – Rice University | ||
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| - | ===== Research groups ===== | ||
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| - | ==== Medical Imaging ==== | ||
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| - | * [[https://www2.warwick.ac.uk/fac/sci/dcs/research/combi/research/bic/|Bioimage Analysis (BIA) Lab at Warwick]] | ||
| - | |||
| - | ==== Medicine ==== | ||
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| - | * [[http://www.unispital-basel.ch/index.php?id=6902&L=4|Universitätspital Basel - Pathologie - Cancer Research]] | ||
| - | |||
| - | ===== Varia ===== | ||
| - | |||
| - | * [[http://pathorama.ch/|Pathorama]] – a platform with useful pathology-related resources (images, courses etc.) | ||
research/computer-aided-histopathology.1582022336.txt.gz · Last modified: 2020/03/25 11:46 (external edit)
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