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Digital Pathology

​5 Ways to Make Histopathology Image Models More Robust to Domain Shifts: Exploring a variety of approaches: stain normalization, color augmentation, adversarial domain adaptation, model adaptation, and finetuning​
5 Ways to Make Histopathology Image Models More Robust to Domain Shifts
Digital Pathology & AI in routine clinical practice:From quality control to primary cancer diagnosis
​https://www.youtube.com/watch?v=7pRmonus9iM​
​Microvisioneer​
Affordable Whole Slide Imaging | Microvisioneer
Microvisioneer
​Argenit​
Ana Sayfa
Argenit - Akıllı Bilişim Teknolojileri
​X-WOW​
X-WOW Whole Slide Scanning System
X-WOW!
​
QuPath
Mac OS için.svsdosyalarını açacak program ararken bulmuştum QuPath'ı.
QuPath'ın validasyonu kolon tümörlerinde CD3, CD8, p53 ve PD-L1 skorlaması yanısıra H&E preparatlarındaki tümör-stroma oranı ile yapılmış. Örnekler TMA üzerinde, kod ile ve otomatik analiz ile skorlanmış. Önemli bir nokta skorlamalar sağ kalım ile de karşılaştırılmış.
​QuPath: Open source software for digital pathology image analysis
Scientific Reports volume 7, Article number: 16878 (2017)
doi:10.1038/s41598-017-17204-5​
QuPath'ın oldukça iyi eğitim dökümanları var:
​https://github.com/qupath/qupath/wiki​
Makaledeki videolar şunlar:
​MOESM2_ESM.mov​
​MOESM3_ESM.mov​
Makalenin referans verdiği diğer dijital analiz araçlarının makaleleri ise şunlar:
​NIH Image to ImageJ: 25 years of image analysis​
​Fiji: an open-source platform for biological-image analysis​
​Icy: an open bioimage informatics platform for extended reproducible research​
​CellProfiler™: free, versatile software for automated biological image analysis​
​OpenSlide: A vendor-neutral software foundation for digital pathology​
​SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images​
​Collaborative analysis of multi-gigapixel imaging data using Cytomine​
​Immunoratio 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. Immunomembrane 'den ise pek iyi sonuç alamamıştım.
​ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67​
​https://digitalpathologyassociation.org/whole-slide-imaging-repository​
​https://digitalpathologyassociation.org/​
Websites
​https://pathpresenter.com/​
​http://www.rosaicollection.org/​
​http://cancer.digitalslidearchive.net/​
Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data
​https://academic.oup.com/jamia/article/20/6/1091/703483​
Johns Hopkins Pathology Unknowns
​https://digital.pathology.johnshopkins.edu/repos/451​
Softwares
​http://www.virasoft.com.tr/​
​http://en.mydigipath.com/​
​https://qupath.github.io/​
​http://www.microvisioneer.com/​
​http://virtualvizyon.com/​
​https://easyzoom.com/​
Easy Scanner
​https://twitter.com/argenitt/status/814824189345624064​
Smartphone Whole Slide Imaging(sWSI) Demo--Low Cost Slide Scanner.
​https://www.youtube.com/watch?v=orcYKy19mjQ​
​https://micro-manager.org/​
Google's interest in digital pathology is very important for our field. See 55th minute
​https://youtu.be/Y2VF8tmLFHw?t=55m11s​
​Assisting Pathologists in Detecting Cancer with Deep Learning​
​https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html​
Detecting Cancer Metastases on Gigapixel Pathology Images
​https://arxiv.org/abs/1703.02442​
Manual Microscope Image Stitching
​https://www.meyerinst.com/digital/image-stitching/​
Motic EASY SCAN PRO Pathology Slide Scanner
​https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/​
​https://www.viewsiq.com/panoptiq​
Metadata matters: access to image data in the real world
​http://jcb.rupress.org/content/189/5/777​
Detecting cancer in real-time with machine learning
​https://www.youtube.com/watch?v=9Mz84cwVmS0​
​An Augmented Reality Microscope for Cancer Detection​
​An Augmented Reality Microscope for Real-time Automated Detection of Cancer​
Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study).
​http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx​
The Gold Standard Paradox in Digital Image Analysis Manual Versus Automated Scoring as Ground Truth
Arch Pathol Lab Med. 2017 May 30. PMID: 28557614 DOI: 10.5858/arpa.2016-0386-RA​
About the Usage of Digital Pathology
Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study).
​http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx​
The Gold Standard Paradox in Digital Image Analysis Manual Versus Automated Scoring as Ground Truth
Arch Pathol Lab Med. 2017 May 30. PMID: 28557614 DOI: 10.5858/arpa.2016-0386-RA​
Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study).
​http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx​
The Gold Standard Paradox in Digital Image Analysis Manual Versus Automated Scoring as Ground Truth
Arch Pathol Lab Med. 2017 May 30. PMID: 28557614 DOI: 10.5858/arpa.2016-0386-RA​
Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study).
​http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx​
The Gold Standard Paradox in Digital Image Analysis Manual Versus Automated Scoring as Ground Truth
Arch Pathol Lab Med. 2017 May 30. PMID: 28557614 DOI: 10.5858/arpa.2016-0386-RA​
Digital Pathology
Mac OS için.svsdosyalarını açacak program ararken bulmuştum QuPath'ı.
QuPath'ın validasyonu kolon tümörlerinde CD3, CD8, p53 ve PD-L1 skorlaması yanısıra H&E preparatlarındaki tümör-stroma oranı ile yapılmış. Örnekler TMA üzerinde, kod ile ve otomatik analiz ile skorlanmış. Önemli bir nokta skorlamalar sağ kalım ile de karşılaştırılmış.
​QuPath: Open source software for digital pathology image analysis
Scientific Reports volume 7, Article number: 16878 (2017)
doi:10.1038/s41598-017-17204-5​
QuPath'ın oldukça iyi eğitim dökümanları var:
​https://github.com/qupath/qupath/wiki​
Makaledeki videolar şunlar:
​MOESM2_ESM.mov​
​MOESM3_ESM.mov​
Makalenin referans verdiği diğer dijital analiz araçlarının makaleleri ise şunlar:
​NIH Image to ImageJ: 25 years of image analysis​
​Fiji: an open-source platform for biological-image analysis​
​Icy: an open bioimage informatics platform for extended reproducible research​
​CellProfiler™: free, versatile software for automated biological image analysis​
​OpenSlide: A vendor-neutral software foundation for digital pathology​
​SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images​
​Collaborative analysis of multi-gigapixel imaging data using Cytomine​
​Immunoratio 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. Immunomembrane 'den ise pek iyi sonuç alamamıştım.
​ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67​
​https://digitalpathologyassociation.org/whole-slide-imaging-repository​
​https://digitalpathologyassociation.org/​
Websites
​https://pathpresenter.com/​
​http://www.rosaicollection.org/​
​http://cancer.digitalslidearchive.net/​
Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data
​https://academic.oup.com/jamia/article/20/6/1091/703483​
Johns Hopkins Pathology Unknowns
​https://digital.pathology.johnshopkins.edu/repos/451​
Softwares
​http://www.virasoft.com.tr/​
​http://en.mydigipath.com/​
​https://qupath.github.io/​
​http://www.microvisioneer.com/​
​http://virtualvizyon.com/​
​https://easyzoom.com/​
Easy Scanner
​https://twitter.com/argenitt/status/814824189345624064​
Smartphone Whole Slide Imaging(sWSI) Demo--Low Cost Slide Scanner.
​https://www.youtube.com/watch?v=orcYKy19mjQ​
​https://micro-manager.org/​
Google's interest in digital pathology is very important for our field. See 55th minute
​https://youtu.be/Y2VF8tmLFHw?t=55m11s​
​Assisting Pathologists in Detecting Cancer with Deep Learning​
​https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html​
Detecting Cancer Metastases on Gigapixel Pathology Images
​https://arxiv.org/abs/1703.02442​
Manual Microscope Image Stitching
​https://www.meyerinst.com/digital/image-stitching/​
Motic EASY SCAN PRO Pathology Slide Scanner
​https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/​
​https://www.viewsiq.com/panoptiq​
Metadata matters: access to image data in the real world
​http://jcb.rupress.org/content/189/5/777​
Detecting cancer in real-time with machine learning
​https://www.youtube.com/watch?v=9Mz84cwVmS0​
​An Augmented Reality Microscope for Cancer Detection​
​An Augmented Reality Microscope for Real-time Automated Detection of Cancer​
Mac OS için.svsdosyalarını açacak program ararken bulmuştum QuPath'ı.
QuPath'ın validasyonu kolon tümörlerinde CD3, CD8, p53 ve PD-L1 skorlaması yanısıra H&E preparatlarındaki tümör-stroma oranı ile yapılmış. Örnekler TMA üzerinde, kod ile ve otomatik analiz ile skorlanmış. Önemli bir nokta skorlamalar sağ kalım ile de karşılaştırılmış.
​QuPath: Open source software for digital pathology image analysis
Scientific Reports volume 7, Article number: 16878 (2017)
doi:10.1038/s41598-017-17204-5​
QuPath'ın oldukça iyi eğitim dökümanları var:
​https://github.com/qupath/qupath/wiki​
Makaledeki videolar şunlar:
​MOESM2_ESM.mov​
​MOESM3_ESM.mov​
Makalenin referans verdiği diğer dijital analiz araçlarının makaleleri ise şunlar:
​NIH Image to ImageJ: 25 years of image analysis​
​Fiji: an open-source platform for biological-image analysis​
​Icy: an open bioimage informatics platform for extended reproducible research​
​CellProfiler™: free, versatile software for automated biological image analysis​
​OpenSlide: A vendor-neutral software foundation for digital pathology​
​SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images​
​Collaborative analysis of multi-gigapixel imaging data using Cytomine​
​Immunoratio 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. Immunomembrane 'den ise pek iyi sonuç alamamıştım.
​ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67​
​https://digitalpathologyassociation.org/whole-slide-imaging-repository​
​https://digitalpathologyassociation.org/​
Websites
​https://pathpresenter.com/​
​http://www.rosaicollection.org/​
​http://cancer.digitalslidearchive.net/​
Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data
​https://academic.oup.com/jamia/article/20/6/1091/703483​
Johns Hopkins Pathology Unknowns
​https://digital.pathology.johnshopkins.edu/repos/451​
Softwares
​http://www.virasoft.com.tr/​
​http://en.mydigipath.com/​
​https://qupath.github.io/​
​http://www.microvisioneer.com/​
​http://virtualvizyon.com/​
​https://easyzoom.com/​
Easy Scanner
​https://twitter.com/argenitt/status/814824189345624064​
Smartphone Whole Slide Imaging(sWSI) Demo--Low Cost Slide Scanner.
​https://www.youtube.com/watch?v=orcYKy19mjQ​
​https://micro-manager.org/​
Google's interest in digital pathology is very important for our field. See 55th minute
​https://youtu.be/Y2VF8tmLFHw?t=55m11s​
​Assisting Pathologists in Detecting Cancer with Deep Learning​
​https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html​
Detecting Cancer Metastases on Gigapixel Pathology Images
​https://arxiv.org/abs/1703.02442​
Manual Microscope Image Stitching
​https://www.meyerinst.com/digital/image-stitching/​
Motic EASY SCAN PRO Pathology Slide Scanner
​https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/​
​https://www.viewsiq.com/panoptiq​
Metadata matters: access to image data in the real world
​http://jcb.rupress.org/content/189/5/777​
Detecting cancer in real-time with machine learning
​https://www.youtube.com/watch?v=9Mz84cwVmS0​
​An Augmented Reality Microscope for Cancer Detection​
​An Augmented Reality Microscope for Real-time Automated Detection of Cancer​
Single slide scanner
​optiscan​