Digital Pathology & AI in routine clinical practice:From quality control to primary cancer diagnosis

​https://www.youtube.com/watch?v=7pRmonus9iM​

​Microvisioneer​

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​Argenit​

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​X-WOW​

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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​