From dee1072f155ae652f9288db8f1ef6578a432b307 Mon Sep 17 00:00:00 2001 From: Serdar Balci Date: Sun, 28 Jul 2024 13:24:07 +0000 Subject: [PATCH] GITBOOK-172: change request with no subject merged in GitBook --- .../digital-pathology.md | 196 +++++++++--------- 1 file changed, 96 insertions(+), 100 deletions(-) diff --git a/computational-digital-and-mathematical-pathology/digital-pathology.md b/computational-digital-and-mathematical-pathology/digital-pathology.md index 011d7cbb..2b3a5679 100644 --- a/computational-digital-and-mathematical-pathology/digital-pathology.md +++ b/computational-digital-and-mathematical-pathology/digital-pathology.md @@ -1,10 +1,10 @@ # 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](https://pixelscientia.com/article-5-ways-to-make-histopathology-image-models-more-robust-to-domain-shifts.html) - +{% embed url="https://www.youtube.com/watch?v=mD3FkPwp2Y4&t=2312s" %} -{% embed url="https://pixelscientia.com/article-5-ways-to-make-histopathology-image-models-more-robust-to-domain-shifts.html" caption="" %} +#### [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](https://pixelscientia.com/article-5-ways-to-make-histopathology-image-models-more-robust-to-domain-shifts.html) +{% embed url="https://pixelscientia.com/article-5-ways-to-make-histopathology-image-models-more-robust-to-domain-shifts.html" %} #### **Digital Pathology & AI in routine clinical practice:From quality control to primary cancer diagnosis** @@ -32,10 +32,10 @@ Mac OS için`.svs`dosyalarını açacak program ararken bulmuştum [QuPath](https://qupath.github.io/)'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'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](https://www.nature.com/articles/s41598-017-17204-5) -> [Scientific Reports volume 7, Article number: 16878 \(2017\)](https://www.nature.com/articles/s41598-017-17204-5) +> [QuPath: Open source software for digital pathology image analysis](https://www.nature.com/articles/s41598-017-17204-5)\ +> [Scientific Reports volume 7, Article number: 16878 (2017)](https://www.nature.com/articles/s41598-017-17204-5)\ > [doi:10.1038/s41598-017-17204-5](https://www.nature.com/articles/s41598-017-17204-5) QuPath'ın oldukça iyi eğitim dökümanları var: @@ -44,27 +44,27 @@ QuPath'ın oldukça iyi eğitim dökümanları var: Makaledeki videolar şunlar: -[MOESM2_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598_2017_17204_MOESM2_ESM.mov) +[MOESM2\_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598\_2017\_17204\_MOESM2\_ESM.mov) -[MOESM3_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598_2017_17204_MOESM3_ESM.mov) +[MOESM3\_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598\_2017\_17204\_MOESM3\_ESM.mov) Makalenin referans verdiği diğer dijital analiz araçlarının makaleleri ise şunlar: -- [NIH Image to ImageJ: 25 years of image analysis](https://www.nature.com/articles/nmeth.2089) -- [Fiji: an open-source platform for biological-image analysis](https://www.nature.com/articles/nmeth.2019) -- [Icy: an open bioimage informatics platform for extended reproducible research](https://www.nature.com/articles/nmeth.2075) -- [CellProfiler™: free, versatile software for automated biological image analysis](https://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/January/CellProfiler-free-versatile-software-for-automated-biological-image-analysis/biotechniques-40380.html) -- [OpenSlide: A vendor-neutral software foundation for digital pathology](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2013;volume=4;issue=1;spage=27;epage=27;aulast=Goode) -- [SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289) -- [Collaborative analysis of multi-gigapixel imaging data using Cytomine](https://academic.oup.com/bioinformatics/article/32/9/1395/1744553) -- [Immunoratio](http://jvsmicroscope.uta.fi/immunoratio/) 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. [Immunomembrane](http://jvsmicroscope.uta.fi/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://breast-cancer-research.biomedcentral.com/articles/10.1186/bcr2615) +* [NIH Image to ImageJ: 25 years of image analysis](https://www.nature.com/articles/nmeth.2089) +* [Fiji: an open-source platform for biological-image analysis](https://www.nature.com/articles/nmeth.2019) +* [Icy: an open bioimage informatics platform for extended reproducible research](https://www.nature.com/articles/nmeth.2075) +* [CellProfiler™: free, versatile software for automated biological image analysis](https://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/January/CellProfiler-free-versatile-software-for-automated-biological-image-analysis/biotechniques-40380.html) +* [OpenSlide: A vendor-neutral software foundation for digital pathology](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2013;volume=4;issue=1;spage=27;epage=27;aulast=Goode) +* [SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289) +* [Collaborative analysis of multi-gigapixel imaging data using Cytomine](https://academic.oup.com/bioinformatics/article/32/9/1395/1744553) +* [Immunoratio](http://jvsmicroscope.uta.fi/immunoratio/) 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. [Immunomembrane](http://jvsmicroscope.uta.fi/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://breast-cancer-research.biomedcentral.com/articles/10.1186/bcr2615) [https://digitalpathologyassociation.org/whole-slide-imaging-repository](https://digitalpathologyassociation.org/whole-slide-imaging-repository) [https://digitalpathologyassociation.org/](https://digitalpathologyassociation.org/) -- Websites +* Websites [https://pathpresenter.com/](https://pathpresenter.com/) @@ -76,11 +76,11 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [https://academic.oup.com/jamia/article/20/6/1091/703483](https://academic.oup.com/jamia/article/20/6/1091/703483) -- Johns Hopkins Pathology Unknowns +* Johns Hopkins Pathology Unknowns [https://digital.pathology.johnshopkins.edu/repos/451](https://digital.pathology.johnshopkins.edu/repos/451) -- Softwares +* Softwares [http://www.virasoft.com.tr/](http://www.virasoft.com.tr/) @@ -94,43 +94,43 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [https://easyzoom.com/](https://easyzoom.com/) -- Easy Scanner +* Easy Scanner [https://twitter.com/argenitt/status/814824189345624064](https://twitter.com/argenitt/status/814824189345624064) -- Smartphone Whole Slide Imaging\(sWSI\) Demo--Low Cost Slide Scanner. +* Smartphone Whole Slide Imaging(sWSI) Demo--Low Cost Slide Scanner. [https://www.youtube.com/watch?v=orcYKy19mjQ](https://www.youtube.com/watch?v=orcYKy19mjQ) [https://micro-manager.org/](https://micro-manager.org/) -- Google's interest in digital pathology is very important for our field. See 55th minute +* Google's interest in digital pathology is very important for our field. See 55th minute [https://youtu.be/Y2VF8tmLFHw?t=55m11s](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) +* [Assisting Pathologists in Detecting Cancer with Deep Learning](https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html) [https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html](https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html) -- Detecting Cancer Metastases on Gigapixel Pathology Images +* Detecting Cancer Metastases on Gigapixel Pathology Images [https://arxiv.org/abs/1703.02442](https://arxiv.org/abs/1703.02442) -- Manual Microscope Image Stitching +* Manual Microscope Image Stitching [https://www.meyerinst.com/digital/image-stitching/](https://www.meyerinst.com/digital/image-stitching/) -- Motic EASY SCAN PRO Pathology Slide Scanner +* Motic EASY SCAN PRO Pathology Slide Scanner [https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/](https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/) [https://www.viewsiq.com/panoptiq](https://www.viewsiq.com/panoptiq) -- Metadata matters: access to image data in the real world +* Metadata matters: access to image data in the real world [http://jcb.rupress.org/content/189/5/777](http://jcb.rupress.org/content/189/5/777) -- Detecting cancer in real-time with machine learning +* Detecting cancer in real-time with machine learning [https://www.youtube.com/watch?v=9Mz84cwVmS0](https://www.youtube.com/watch?v=9Mz84cwVmS0) @@ -138,37 +138,37 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [An Augmented Reality Microscope for Real-time Automated Detection of Cancer](https://drive.google.com/open?id=1WRBCqJItaGly-9PDSMlwQ5Ldhc8lB0lf) -- Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases \(Pivotal Study\). +* 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](http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx) +[http://journals.lww.com/ajsp/Abstract/publishahead/Whole\_Slide\_Imaging\_Versus\_Microscopy\_for\_Primary.97978.aspx](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 +* 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](https://doi.org/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 \(Pivotal Study\). +* 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](http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx) +[http://journals.lww.com/ajsp/Abstract/publishahead/Whole\_Slide\_Imaging\_Versus\_Microscopy\_for\_Primary.97978.aspx](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 +* 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](https://doi.org/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 \(Pivotal Study\). +* 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](http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx) +[http://journals.lww.com/ajsp/Abstract/publishahead/Whole\_Slide\_Imaging\_Versus\_Microscopy\_for\_Primary.97978.aspx](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 +* 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](https://doi.org/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 \(Pivotal Study\). +* 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](http://journals.lww.com/ajsp/Abstract/publishahead/Whole_Slide_Imaging_Versus_Microscopy_for_Primary.97978.aspx) +[http://journals.lww.com/ajsp/Abstract/publishahead/Whole\_Slide\_Imaging\_Versus\_Microscopy\_for\_Primary.97978.aspx](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 +* 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](https://doi.org/10.5858/arpa.2016-0386-RA) @@ -176,10 +176,10 @@ Arch Pathol Lab Med. 2017 May 30. PMID: 28557614 DOI: [10.5858/arpa.2016-0386-RA Mac OS için`.svs`dosyalarını açacak program ararken bulmuştum [QuPath](https://qupath.github.io/)'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'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](https://www.nature.com/articles/s41598-017-17204-5) -> [Scientific Reports volume 7, Article number: 16878 \(2017\)](https://www.nature.com/articles/s41598-017-17204-5) +> [QuPath: Open source software for digital pathology image analysis](https://www.nature.com/articles/s41598-017-17204-5)\ +> [Scientific Reports volume 7, Article number: 16878 (2017)](https://www.nature.com/articles/s41598-017-17204-5)\ > [doi:10.1038/s41598-017-17204-5](https://www.nature.com/articles/s41598-017-17204-5) QuPath'ın oldukça iyi eğitim dökümanları var: @@ -188,27 +188,27 @@ QuPath'ın oldukça iyi eğitim dökümanları var: Makaledeki videolar şunlar: -[MOESM2_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598_2017_17204_MOESM2_ESM.mov) +[MOESM2\_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598\_2017\_17204\_MOESM2\_ESM.mov) -[MOESM3_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598_2017_17204_MOESM3_ESM.mov) +[MOESM3\_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598\_2017\_17204\_MOESM3\_ESM.mov) Makalenin referans verdiği diğer dijital analiz araçlarının makaleleri ise şunlar: -- [NIH Image to ImageJ: 25 years of image analysis](https://www.nature.com/articles/nmeth.2089) -- [Fiji: an open-source platform for biological-image analysis](https://www.nature.com/articles/nmeth.2019) -- [Icy: an open bioimage informatics platform for extended reproducible research](https://www.nature.com/articles/nmeth.2075) -- [CellProfiler™: free, versatile software for automated biological image analysis](https://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/January/CellProfiler-free-versatile-software-for-automated-biological-image-analysis/biotechniques-40380.html) -- [OpenSlide: A vendor-neutral software foundation for digital pathology](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2013;volume=4;issue=1;spage=27;epage=27;aulast=Goode) -- [SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289) -- [Collaborative analysis of multi-gigapixel imaging data using Cytomine](https://academic.oup.com/bioinformatics/article/32/9/1395/1744553) -- [Immunoratio](http://jvsmicroscope.uta.fi/immunoratio/) 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. [Immunomembrane](http://jvsmicroscope.uta.fi/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://breast-cancer-research.biomedcentral.com/articles/10.1186/bcr2615) +* [NIH Image to ImageJ: 25 years of image analysis](https://www.nature.com/articles/nmeth.2089) +* [Fiji: an open-source platform for biological-image analysis](https://www.nature.com/articles/nmeth.2019) +* [Icy: an open bioimage informatics platform for extended reproducible research](https://www.nature.com/articles/nmeth.2075) +* [CellProfiler™: free, versatile software for automated biological image analysis](https://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/January/CellProfiler-free-versatile-software-for-automated-biological-image-analysis/biotechniques-40380.html) +* [OpenSlide: A vendor-neutral software foundation for digital pathology](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2013;volume=4;issue=1;spage=27;epage=27;aulast=Goode) +* [SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289) +* [Collaborative analysis of multi-gigapixel imaging data using Cytomine](https://academic.oup.com/bioinformatics/article/32/9/1395/1744553) +* [Immunoratio](http://jvsmicroscope.uta.fi/immunoratio/) 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. [Immunomembrane](http://jvsmicroscope.uta.fi/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://breast-cancer-research.biomedcentral.com/articles/10.1186/bcr2615) [https://digitalpathologyassociation.org/whole-slide-imaging-repository](https://digitalpathologyassociation.org/whole-slide-imaging-repository) [https://digitalpathologyassociation.org/](https://digitalpathologyassociation.org/) -- Websites +* Websites [https://pathpresenter.com/](https://pathpresenter.com/) @@ -220,11 +220,11 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [https://academic.oup.com/jamia/article/20/6/1091/703483](https://academic.oup.com/jamia/article/20/6/1091/703483) -- Johns Hopkins Pathology Unknowns +* Johns Hopkins Pathology Unknowns [https://digital.pathology.johnshopkins.edu/repos/451](https://digital.pathology.johnshopkins.edu/repos/451) -- Softwares +* Softwares [http://www.virasoft.com.tr/](http://www.virasoft.com.tr/) @@ -238,43 +238,43 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [https://easyzoom.com/](https://easyzoom.com/) -- Easy Scanner +* Easy Scanner [https://twitter.com/argenitt/status/814824189345624064](https://twitter.com/argenitt/status/814824189345624064) -- Smartphone Whole Slide Imaging\(sWSI\) Demo--Low Cost Slide Scanner. +* Smartphone Whole Slide Imaging(sWSI) Demo--Low Cost Slide Scanner. [https://www.youtube.com/watch?v=orcYKy19mjQ](https://www.youtube.com/watch?v=orcYKy19mjQ) [https://micro-manager.org/](https://micro-manager.org/) -- Google's interest in digital pathology is very important for our field. See 55th minute +* Google's interest in digital pathology is very important for our field. See 55th minute [https://youtu.be/Y2VF8tmLFHw?t=55m11s](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) +* [Assisting Pathologists in Detecting Cancer with Deep Learning](https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html) [https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html](https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html) -- Detecting Cancer Metastases on Gigapixel Pathology Images +* Detecting Cancer Metastases on Gigapixel Pathology Images [https://arxiv.org/abs/1703.02442](https://arxiv.org/abs/1703.02442) -- Manual Microscope Image Stitching +* Manual Microscope Image Stitching [https://www.meyerinst.com/digital/image-stitching/](https://www.meyerinst.com/digital/image-stitching/) -- Motic EASY SCAN PRO Pathology Slide Scanner +* Motic EASY SCAN PRO Pathology Slide Scanner [https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/](https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/) [https://www.viewsiq.com/panoptiq](https://www.viewsiq.com/panoptiq) -- Metadata matters: access to image data in the real world +* Metadata matters: access to image data in the real world [http://jcb.rupress.org/content/189/5/777](http://jcb.rupress.org/content/189/5/777) -- Detecting cancer in real-time with machine learning +* Detecting cancer in real-time with machine learning [https://www.youtube.com/watch?v=9Mz84cwVmS0](https://www.youtube.com/watch?v=9Mz84cwVmS0) @@ -284,10 +284,10 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s Mac OS için`.svs`dosyalarını açacak program ararken bulmuştum [QuPath](https://qupath.github.io/)'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'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](https://www.nature.com/articles/s41598-017-17204-5) -> [Scientific Reports volume 7, Article number: 16878 \(2017\)](https://www.nature.com/articles/s41598-017-17204-5) +> [QuPath: Open source software for digital pathology image analysis](https://www.nature.com/articles/s41598-017-17204-5)\ +> [Scientific Reports volume 7, Article number: 16878 (2017)](https://www.nature.com/articles/s41598-017-17204-5)\ > [doi:10.1038/s41598-017-17204-5](https://www.nature.com/articles/s41598-017-17204-5) QuPath'ın oldukça iyi eğitim dökümanları var: @@ -296,27 +296,27 @@ QuPath'ın oldukça iyi eğitim dökümanları var: Makaledeki videolar şunlar: -[MOESM2_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598_2017_17204_MOESM2_ESM.mov) +[MOESM2\_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598\_2017\_17204\_MOESM2\_ESM.mov) -[MOESM3_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598_2017_17204_MOESM3_ESM.mov) +[MOESM3\_ESM.mov](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-017-17204-5/MediaObjects/41598\_2017\_17204\_MOESM3\_ESM.mov) Makalenin referans verdiği diğer dijital analiz araçlarının makaleleri ise şunlar: -- [NIH Image to ImageJ: 25 years of image analysis](https://www.nature.com/articles/nmeth.2089) -- [Fiji: an open-source platform for biological-image analysis](https://www.nature.com/articles/nmeth.2019) -- [Icy: an open bioimage informatics platform for extended reproducible research](https://www.nature.com/articles/nmeth.2075) -- [CellProfiler™: free, versatile software for automated biological image analysis](https://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/January/CellProfiler-free-versatile-software-for-automated-biological-image-analysis/biotechniques-40380.html) -- [OpenSlide: A vendor-neutral software foundation for digital pathology](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2013;volume=4;issue=1;spage=27;epage=27;aulast=Goode) -- [SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289) -- [Collaborative analysis of multi-gigapixel imaging data using Cytomine](https://academic.oup.com/bioinformatics/article/32/9/1395/1744553) -- [Immunoratio](http://jvsmicroscope.uta.fi/immunoratio/) 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. [Immunomembrane](http://jvsmicroscope.uta.fi/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://breast-cancer-research.biomedcentral.com/articles/10.1186/bcr2615) +* [NIH Image to ImageJ: 25 years of image analysis](https://www.nature.com/articles/nmeth.2089) +* [Fiji: an open-source platform for biological-image analysis](https://www.nature.com/articles/nmeth.2019) +* [Icy: an open bioimage informatics platform for extended reproducible research](https://www.nature.com/articles/nmeth.2075) +* [CellProfiler™: free, versatile software for automated biological image analysis](https://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/January/CellProfiler-free-versatile-software-for-automated-biological-image-analysis/biotechniques-40380.html) +* [OpenSlide: A vendor-neutral software foundation for digital pathology](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2013;volume=4;issue=1;spage=27;epage=27;aulast=Goode) +* [SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289) +* [Collaborative analysis of multi-gigapixel imaging data using Cytomine](https://academic.oup.com/bioinformatics/article/32/9/1395/1744553) +* [Immunoratio](http://jvsmicroscope.uta.fi/immunoratio/) 'yu rutin tanılarda ben kullanıyordum. Elbette tanı için direk oradaki çıkan sayıyı vermiyordum ama kendimi eğitmek için iyi bir araçtı. [Immunomembrane](http://jvsmicroscope.uta.fi/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://breast-cancer-research.biomedcentral.com/articles/10.1186/bcr2615) [https://digitalpathologyassociation.org/whole-slide-imaging-repository](https://digitalpathologyassociation.org/whole-slide-imaging-repository) [https://digitalpathologyassociation.org/](https://digitalpathologyassociation.org/) -- Websites +* Websites [https://pathpresenter.com/](https://pathpresenter.com/) @@ -328,11 +328,11 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [https://academic.oup.com/jamia/article/20/6/1091/703483](https://academic.oup.com/jamia/article/20/6/1091/703483) -- Johns Hopkins Pathology Unknowns +* Johns Hopkins Pathology Unknowns [https://digital.pathology.johnshopkins.edu/repos/451](https://digital.pathology.johnshopkins.edu/repos/451) -- Softwares +* Softwares [http://www.virasoft.com.tr/](http://www.virasoft.com.tr/) @@ -346,43 +346,43 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [https://easyzoom.com/](https://easyzoom.com/) -- Easy Scanner +* Easy Scanner [https://twitter.com/argenitt/status/814824189345624064](https://twitter.com/argenitt/status/814824189345624064) -- Smartphone Whole Slide Imaging\(sWSI\) Demo--Low Cost Slide Scanner. +* Smartphone Whole Slide Imaging(sWSI) Demo--Low Cost Slide Scanner. [https://www.youtube.com/watch?v=orcYKy19mjQ](https://www.youtube.com/watch?v=orcYKy19mjQ) [https://micro-manager.org/](https://micro-manager.org/) -- Google's interest in digital pathology is very important for our field. See 55th minute +* Google's interest in digital pathology is very important for our field. See 55th minute [https://youtu.be/Y2VF8tmLFHw?t=55m11s](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) +* [Assisting Pathologists in Detecting Cancer with Deep Learning](https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html) [https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html](https://research.googleblog.com/2017/03/assisting-pathologists-in-detecting.html) -- Detecting Cancer Metastases on Gigapixel Pathology Images +* Detecting Cancer Metastases on Gigapixel Pathology Images [https://arxiv.org/abs/1703.02442](https://arxiv.org/abs/1703.02442) -- Manual Microscope Image Stitching +* Manual Microscope Image Stitching [https://www.meyerinst.com/digital/image-stitching/](https://www.meyerinst.com/digital/image-stitching/) -- Motic EASY SCAN PRO Pathology Slide Scanner +* Motic EASY SCAN PRO Pathology Slide Scanner [https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/](https://www.meyerinst.com/motic-easy-scan-pro-digital-slide-scanner/) [https://www.viewsiq.com/panoptiq](https://www.viewsiq.com/panoptiq) -- Metadata matters: access to image data in the real world +* Metadata matters: access to image data in the real world [http://jcb.rupress.org/content/189/5/777](http://jcb.rupress.org/content/189/5/777) -- Detecting cancer in real-time with machine learning +* Detecting cancer in real-time with machine learning [https://www.youtube.com/watch?v=9Mz84cwVmS0](https://www.youtube.com/watch?v=9Mz84cwVmS0) @@ -390,16 +390,12 @@ Cancer Digital Slide Archive: an informatics resource to support integrated in s [An Augmented Reality Microscope for Real-time Automated Detection of Cancer](https://drive.google.com/open?id=1WRBCqJItaGly-9PDSMlwQ5Ldhc8lB0lf) ---- +*** -- Single slide scanner +* Single slide scanner [optiscan](https://www.blabmarket.com/urun/optika-optiscan-dijital-mikroskop-tarayici) - ---- - +*** {% embed url="https://www.youtube.com/watch?v=zNRxF-TqUnI" %} - -