miscellaneous
Miscellaneous links to be organised. Ordan burdan derlenmiş ama düzenlenmemiş güncel patoloji içerikleri. https://www.parapathology.com/appendix/miscellaneous
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Miscellaneous links to be organised. Ordan burdan derlenmiş ama düzenlenmemiş güncel patoloji içerikleri. https://www.parapathology.com/appendix/miscellaneous
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https://www.parapathology.com/appendix/miscellaneous
Adenomyoma/adenomyomatosis-associated mural intracholecystic neoplasms: analysis of clinico-pathologic, imaging, and molecular features of a consecutive case series https://link.springer.com/article/10.1007/s00428-025-04077-7
Multiplex Immunohistochemistry and Immunofluorescence: A Practical Update for Pathologists https://www.modernpathology.org/article/S0893-3952(23)00102-3/fulltext
https://github.com/Slicer/Slicer
https://github.com/gaoyi/SlicerBigImage
https://slicerscope.github.io/documents.html
https://www.youtube.com/watch?v=oHwHXa_ROqs
Malatya’dan Boston’a bilim köprüsü https://vimeo.com/880168375
Digital mapping of resected cancer specimens: The visual pathology report https://www.sciencedirect.com/science/article/pii/S2153353924000385
Implementing digital pathology: qualitative and financial insights from eight leading European laboratories https://link.springer.com/article/10.1007/s00428-025-04064-y
Robust sensitivity control in digital pathology via tile score distribution matching https://arxiv.org/abs/2502.20144
Distilling foundation models for robust and efficient models in digital pathology https://arxiv.org/abs/2501.16239
The Future of Immunohistochemistry https://isimm.org/education/isimm-webinars/the-future-of-immunohistochemistry/
ISIMM Webinar - Clinical Implementation of Multiplex IHC/IF with Real World Diagnostic and Predictive Applications with Sanjay Patel https://isimm.us7.list-manage.com/track/click?u=8666755584e8326e820fac159&id=8a9149050a&e=01f46d65a4
EScoP Course on Genitourinary Pathology https://esp-pathology.glueup.com/event/escop-course-on-genitourinary-pathology-135487/
15 Mart Cumartesi günü Koç Üniversitesi hastanesi RMK AIMES Merkezinde gerçekleştirilecek “HPB Cerrahları için Pankreas Patolojisi” Kursu E-AHPBA tarafında “Silver Seal Endorsement” desteği almıştır. Toplantı E-AHPBA tarafından da yayınlanacak olup sunumlar İngilizce gerçekleşecektir. Bölgesel toplantılarda olduğu gibi Zoom ve Youtube üzerinden yayınlanacak canlı yayın ülke genelinde takip edilebilecektir. Toplantı programı ve linklerine web sayfamızdan da (www.hpb.org.tr) ulaşabilirsiniz. Gündelik pratiğimizde pankreas hastalıklarının tanısında deneyimlediğimiz tüm güçlükleri patolojik, endoskopik, radyolojik ve cerrahi açıdan derinlemesine tartışma imkanı bulacağımız bu toplantıya yüz yüze katılma imkanı olan üyelerimizin gtellioglu@kuh.ku.edu.tr adresine mail atmasını rica ediyoruz. Toplantıya katılım ücretsizdir. Toplantı başlığı cerrahlar için olsa da pankreas alanında multidisipliner çalışma zorunluluğu nedeniyle radyolog, endoskopist ve patolog meslektaşlarımızın katılımı ile daha üretken bir toplantı olabileceği inancındayız. Saygılarımızla. Gürkan Tellioğlu Türk HPB Cerrahi Derneği Genel Sekreteri TOPLANTI PROGRAMI
Toplantı linkleri:Zoom link: https://us02web.zoom.us/j/84663332415 YouTube link: https://youtube.com/live/hK_zUh-ZgCM?feature=share
A persistent gender pay gap among faculty in a public university system https://www.nature.com/articles/s41598-024-72871-5
Generative Artificial Intelligence in Anatomic Pathology https://pubmed.ncbi.nlm.nih.gov/39836377/
Reproducible image-based profiling with Pycytominer https://www.nature.com/articles/s41592-025-02611-8
ggplot2 extenders https://ggplot2-extenders.github.io/ggplot-extension-club/meetings.html https://github.com/ggplot2-extenders/ggplot-extension-club/discussions
Multimodal histopathologic models stratify hormone receptor-positive early breast cancer https://www.nature.com/articles/s41467-025-57283-x
SPIDER (Supervised Pathology Image-DEscription Repository) https://www.linkedin.com/posts/activity-7302773428653047809-i1fM/?utm_source=share&utm_medium=member_desktop&rcm=ACoAACHBWocBNSBVkkJY2Vg1Kdp2kTEw1dx44qg https://github.com/HistAI/SPIDER https://huggingface.co/histai https://arxiv.org/abs/2503.02876
https://www.cancergrandchallenges.org/ai-human-collaborations-in-cancer
Hastaların %53'ü müdavi hekiminden daha önce patoloji raporlarına ulaşmış. Bunun sıkıntılı yanları da var. - Az görülen tümörlerde klinisyenin kendini hazırlamaya, patologla istişare etmeye vakti olmalı. Bazen bu şekilde yaptığımız mini klinikopatolojik değerlendirmeler ile raporları ayrıntılandırdığımız ya da düzenlediğimiz oluyor. Hastaya son kararın tek seferde bildirilmesi daha iyi olabiliyor. - Bazı kavramlar hastalarda gereksiz anksiyeteye neden olabiliyor. "Dev hücre" gibi. Google hekimliği bitti, şimdi yapay zekadan raporu analiz ettirmeye başladılar. - Raporda geçen teknik terimler "takibe alındı", "yeni parça", "yeni kesit" bağlamından koparılınca yanlış anlaşılabiliyor. https://www.linkedin.com/posts/jason-wasserman-7a9ba8250_if-you-provide-them-they-will-come-activity-7302428086027837440-Loun?utm_source=share&utm_medium=member_desktop&rcm=ACoAACHBWocBNSBVkkJY2Vg1Kdp2kTEw1dx44qg https://pubmed.ncbi.nlm.nih.gov/40015956/
2023 Classic Lectures in Pathology: What You Need to Know: Lung Pathology - A CME Teaching Activity https://www.youtube.com/watch?v=du7Y6nfKwd8
Pathology in the artificial intelligence era: Guiding innovation and implementation to preserve human insight https://www.sciencedirect.com/science/article/pii/S2374289525000089
Multimodal histopathologic models stratify hormone receptor-positive early breast cancer https://www.nature.com/articles/s41467-025-57283-x
On the Importance of Text Preprocessing for Multimodal Representation Learning and Pathology Report Generation https://arxiv.org/abs/2502.19285
Pathology Report Generation and Multimodal Representation Learning for Cutaneous Melanocytic Lesions https://arxiv.org/abs/2502.19293
GrandQC - A comprehensive solution to quality control in digital pathology: Zhilong Weng, 03/03/25 https://www.youtube.com/watch?v=eWO2gujT7Sw&ab_channel=TIAWarwick
Adam daha retikülini oturtamamış, bana PD-L1 için app kullanın daha rahat cut-off tespit edersiniz diyor.
A pathologist's guide for the diagnostic workup of paediatric central nervous system tumours https://pubmed.ncbi.nlm.nih.gov/39658395/ https://www.pathologyjournal.rcpa.edu.au/action/showPdf?pii=S0031-3025%2824%2900290-3
Foundation Models -- A Panacea for Artificial Intelligence in Pathology? https://arxiv.org/abs/2502.21264
A bottom-up initiated digital external quality assessment scheme for the state-of-the-art pathology in Sweden: reduced variability between pathology departments https://link.springer.com/article/10.1007/s00428-025-04059-9
Microsoft Dragon Copilot provides the healthcare industry’s first unified voice AI assistant that enables clinicians to streamline clinical documentation, surface information and automate tasks https://news.microsoft.com/2025/03/03/microsoft-dragon-copilot-provides-the-healthcare-industrys-first-unified-voice-ai-assistant-that-enables-clinicians-to-streamline-clinical-documentation-surface-information-and-automate-task/
AANP Teaching Rounds - February 26, 2025 - PitNET/Pituitary Adenoma Classification: Survival Tips https://www.youtube.com/watch?v=5ZqV2QnIbaA&ab_channel=AmericanAssociationofNeuropathologists
2 Mart 2025. Sosyal medyada paylaşılanlara göre PubMed erişiminde aksaklıklar yaşanıyormuş. Eskiden hemen her Amerikan fedeal bütçesinin askıda kaldığı dönemde güncellemelere ara verilirdi. Ama bu derecede erişim sıkıntısını hiç görmemiştim. Yıllar önce PubMed abstract'larını sistematik bir şekilde -yine PubMed'in sağladığı entrez araçlarıyla- indirip kaydetmiştim. O dönemlerde daha Large Language Modeller yoktu ama "write your own book" kodlu projeler üzerinde çalışıyorduk. https://github.com/sbalci/bibliometrics Sonra işte olanlar oldu, ölenler öldü. Projeler ve hayaller akim kaldı. Halbuki bugün bir PubMed mirror'u yapabilmemiz mümkündü. Bir tür "içimde kalanlar" ya da "ukdeler CV"si hazırlayayım bari ...
2 Mart 2025. Olayın kök nedenine bakmak lazım. Bu adamlar ne "mal sahibi" ne de "işi yapan" kişiler. Bir dönem işin erbabı olan, ama zaman içinde yeniliklere ayak uyduramadığı için artık o işi yapamayanlar, tecrübelerinden istifade edilmek üzere bir tür "ara müdür" olarak hayatlarını sürdürebilirler. Peter principle da değil, onlar da başka, bunlar da başka. Bunlar "profesyonel yönetici" olduklarını iddia eden, ne işin mutfağında çalışmış ne de malın sahibi olmayan, bugün bir şirkette başka bir gün başka bir şirkette yer alabilecek, "plaza dili" ile tekellüm eden, C-Level olarak kendilerini tanımlayanlar. Ara müdürlerin en işe yaramaz olanları. İşi bilmedikleri için, o işin mutfağı ile uğraşamazlar. Boş görünmemek için de kendilerine meşgale icat ederler. Kurumsal mesaj yayınlamak ya da yayımlamamak ya da yayımlayanlara had bildirmek ya da o kurumsal mesajda kullanılan rengin fontunu belirlemek gibi. Bunların en "prestijli" olanlarını 8 Mart'ta yayınlayacakları mesajlarda görürsünüz. Kadın çalışanlarına gebelik ve süt izni vermez, "bu bekar yakında evlenir gider" diye iş vermez, kadınlara daha ucuz maaş verir, ama 8 Mart'ta ünlü birkaç kişi ile poz ve mesaj verirler. Yani olayın özüyle bu ayın bir ilgisi yok. Zaten bu ayda sevinebilmek biraz da nasip işi, o apayrı bir şey. Heman Mevlam cümlemize selamet versin, mal ve iş sahiplerini bu C-level'ların şerrinden halas eylesin.
Digital counting of tissue cells for molecular analysis: the QuANTUM pipeline https://link.springer.com/article/10.1007/s00428-024-03794-9
The National Pathology Imaging Co-operative (NPIC) have created an open source public register of AI based pathology tools to support the implementation of AI in diagnostic services. https://www.rcpath.org/discover-pathology/news/firstofitskindcentralresourceofaibasedpathologytoolslaunched.html
Public evidence on AI products for digital pathology https://www.nature.com/articles/s41746-024-01294-3
Register of AI products for digital pathology https://osf.io/ypajd
Blueprints from plane to space: outlook of next-generation three-dimensional histopathology https://onlinelibrary.wiley.com/doi/10.1111/cas.16095
CUBIC pathology: three-dimensional imaging for pathological diagnosis https://www.nature.com/articles/s41598-017-09117-0
Foundation Models in Pathology: A Major Leap Forward https://www.linkedin.com/posts/mohsinbilal_foundation-models-in-pathology-a-major-leap-activity-7238134088606334976-yLHH/
Foundation Models in Computational Pathology: A Review of Challenges, Opportunities, and Impact https://arxiv.org/abs/2502.08333
Introduction to Artificial Intelligence and Machine Learning in Pathology and Medicine: Generative and Nongenerative Artificial Intelligence Basics https://www.modernpathology.org/article/S0893-3952(24)00268-0/fulltext
AI-Driven Spatial Transcriptomics Unlocks Large-Scale Breast Cancer Biomarker Discovery from Histopathology https://www.biorxiv.org/content/10.1101/2024.10.16.618609v2
Annotation Practices in Computational Pathology: A European Society of Digital and Integrative Pathology (ESDIP) Survey Study https://doi.org/10.1016/j.labinv.2024.102203
The tumour histopathology “glossary” for AI developers https://doi.org/10.1371/journal.pcbi.1012708
An international study of stain variability in histopathology using qualitative and quantitative analysis https://www.sciencedirect.com/science/article/pii/S2153353925000057
https://x.com/AI4Pathology/status/1889713583321190819
Artificial intelligence in digital pathology — time for a reality check https://www.nature.com/articles/s41571-025-00991-6
When Doctors With A.I. Are Outperformed by A.I. Alone https://erictopol.substack.com/p/when-doctors-with-ai-are-outperformed
Current Pathology Foundation Models are unrobust to Medical Center Differences https://arxiv.org/abs/2501.18055
qupath-extension-gncnn https://github.com/UCLM-VISILAB/qupath-extension-gncnn
GNCnn: A QuPath extension for glomerulosclerosis and glomerulonephritis characterization based on deep learning https://www.sciencedirect.com/science/article/pii/S2001037024004197
Frontiers in Computational Pathology https://sites.google.com/view/miua2025-fcpath/
A comprehensive evaluation of histopathology foundation models for ovarian cancer subtype classification https://www.nature.com/articles/s41698-025-00799-8
https://www.youtube.com/watch?v=984Jz2QCvng
Developing an AI tool for renal pathology: case Galileo https://www.aiforia.com/webinar-galileo-ai-tool-for-renal-pathology
Paige PanCancer Detect: A Milestone Achieved in Computational Pathology! https://www.linkedin.com/pulse/paige-pancancer-detect-milestone-achieved-pathology-siqi-liu-mgume/
Overcoming Challenges in Implementing Digital Pathology and AI at Scale: Lessons from the Field https://www.linkedin.com/pulse/overcoming-challenges-implementing-digital-pathology-ai-singh-md-nd4se/
Modella AI’s Generative AI Co-Pilot PathChat Receives FDA Breakthrough Device Designation https://www.businesswire.com/news/home/20250128288933/en/Modella-AI%E2%80%99s-Generative-AI-Co-Pilot-PathChat-Receives-FDA-Breakthrough-Device-Designation
Artificial Intelligence–Based Classification of Renal Oncocytic Neoplasms https://allen.silverchair-cdn.com/allen/content_public/journal/aplm/pap/10.5858_arpa.2024-0374-oa/3/10.5858_arpa.2024-0374-oa.pdf?Expires=1743260269&Signature=nU8t8JqwgbmA8urWjtZbdDFQZFuycpkmp5kJYlufdwSBUFrtUAAAeHqJiNY5zJWnbw0MnjReeMWlXlusM3U-OIRbs68fE2xMlSdwpV49ElAwnLDjJUIEslO16DTF33z9FHkGWLPDFcnDkdRRMBNMSPfU65xrHHCuI6vVQ921X7rVh3528zu02SdlCFmWyx2t1jfjJdq7XFvjGEoYmREL5CvYgJRCMxU34Md08lLjSyg9Ma7CBOszvUVGoDoP7Wd41AeHXM5RpJPWTbrmlo5vbfK1o8exxNkHxwnEJ23onDzg2WkTlTdZwZkm87eMDitnvPfS5E8wahhdKFwQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
https://x.com/Vik_deshpandeMD/status/1556064583915393026
https://x.com/JClinPath_BMJ/status/1893284420355788953
Gene of the month: GATA3 https://jcp.bmj.com/content/76/12/793
https://www.youtube.com/watch?v=OAypMgjhRLE&t=2010s&ab_channel=TIAWarwick
Current role of cytopathology in the molecular and computational era: The perspective of young pathologists https://acsjournals.onlinelibrary.wiley.com/doi/10.1002/cncy.22832
Biyopsi bakarken ben:
Reproducibility of endometrial intraepithelial neoplasia diagnosis is good, but influenced by the diagnostic style of pathologists https://pubmed.ncbi.nlm.nih.gov/22301705/
An international study of stain variability in histopathology using qualitative and quantitative analysis https://www.sciencedirect.com/science/article/pii/S2153353925000057
Comparative performance of PD-L1 scoring by pathologists and AI algorithms https://onlinelibrary.wiley.com/doi/full/10.1111/his.15432
Frontiers in Computational Pathology https://sites.google.com/view/miua2025-fcpath/
FS2K2025 Workshop Introduction https://www.youtube.com/watch?v=Vl9V5PxOQIc
NPIC Digital Pathology Webinar Series - Innovation into Practice - Webinar 8 - Ask Us Anything. The National Pathology Imaging Co-Operative (NPIC) is back with an exciting new series of free educational webinars on digital pathology topics. Learn first-hand about hot topics in clinical digital reporting, the digital laboratory, IT and informatics and get a chance to pose your questions to the experts! Suitable for pathologists, biomedical scientists, informatics and IT professionals, managers and industry representatives. https://events.teams.microsoft.com/event/b46d9cac-a466-4bdf-8076-35617dd24670@37c354b2-85b0-47f5-b222-07b48d774ee3
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics https://www.nature.com/articles/s43018-024-00793-2
Virtual 2025 QuPath Training Course: From Samples to KnowledgeThank you for your interest in our training course! We will broadcast the course in real time on Zoom. While we won't have the ability to directly assist you, we will have a way for you to ask questions which will be reviewed and, if time allows, answered during the course. Please fill out the form below and we will email you the meeting details and zoom link when available. You will also get installation instructions, and links to files, presentations, and projects. The training course will take place on February 24-25, 2025 between 9 and 5 pm PST. We will not stream or record the Advanced User's Meeting on February 26 in order to protect preliminary data. Alternatively, if you want to attend in-person, please register on Eventbrite. We don't spam, sell, or share your information. &#xNAN;We highly recommend using a comfortable mouse with a scroll wheel during the training. https://docs.google.com/forms/d/e/1FAIpQLSdl1lv_5NlYkdz_JtQDb2HEAUbQxajvU7y5IN4PhmtgBXF-ng/viewform
Panik Tanı https://www.youtube.com/watch?v=HFEN9C20ceQ
GI Path 2nd Opinion Club will meet on 2/11 at 8AM EST. Please bring any GI/panc/liver case which you'd like to get opinions about. All cases are welcome. There is no expectation that the cases be "interesting." Please forward to anyone who may be interested. https://zoom.us/j/91358942539?pwd=gs1A5c2Ln3K8d90qV4kRAGjCv1X3T7.1
Artificial intelligence in digital pathology — time for a reality check
https://x.com/AI4Pathology/status/1889713583321190819
https://github.com/mahmoodlab/trident
https://github.com/mahmoodlab/patho-bench
https://github.com/mahmoodlab/UNI
https://github.com/mahmoodlab/TITAN
Accelerating Data Processing and Benchmarking of AI Models for Pathology https://arxiv.org/abs/2502.06750
https://agentlaboratory.github.io/
https://github.com/microsoft/data-formulator
A new vision in Pathology: From clinical implementation of Digital Pathology to algorithm development in Computational Pathology https://repositorio-aberto.up.pt/handle/10216/165284
Digital Pathology in Endocrine Disorders https://link.springer.com/collections/gabfeibadh
A multicenter study to evaluate the analytical precision by pathologists using the Aperio GT 450 DX https://pmc.ncbi.nlm.nih.gov/articles/PMC11600015/
An international study of stain variability in histopathology using qualitative and quantitative analysis https://www.sciencedirect.com/science/article/pii/S2153353925000057#s0040
Tissue Image Analytics (TIA) Centre https://warwick.ac.uk/fac/cross_fac/tia/seminars/seminars-24-25/
When Doctors With A.I. Are Outperformed by A.I. Alone https://erictopol.substack.com/p/when-doctors-with-ai-are-outperformed
Generative Artificial Intelligence in Anatomic Pathology https://pubmed.ncbi.nlm.nih.gov/39836377/
NPIC Digital Pathology Webinar Series - Innovation into Practice - Webinar 7 - A Focus on Stain, Scanner Physical Quality and Display. https://events.teams.microsoft.com/event/0c9807b9-d89b-4e95-b77a-7719fa96d169@37c354b2-85b0-47f5-b222-07b48d774ee3
Gross examination and frozen section of breast pathology and oncology surgery specimens https://www.youtube.com/watch?v=SR-mAuzxt2o
Your Operating System ｜Eukaryotic Transcription https://www.youtube.com/watch?v=HZAmbbTcQ3M&t=16s
https://github.com/mcanouil/quarto-issues-experiments/tree/main/test-statistical-analysis-listing
https://m.canouil.dev/quarto-extensions/
https://gist.github.com/richarddmorey/ba6aa67ef2d38356f12f7e17d0421036
https://cran.r-project.org/web/packages/staticryptR/readme/README.html
https://compgenomr.github.io/book/
https://youtube.com/playlist?list=PL3x6DOfs2NGjAvuW2kC0kKP_oCWK2omFt&si=mhWs0jII7ipJ56cf
https://youtube.com/playlist?list=PL3x6DOfs2NGj2sMp67G5ihOyiY4d1VVvr&si=JCqObGzE00qUQt5C
What can men do against such reckless hate https://www.youtube.com/watch?v=t6qQSll7InQ
Bu federasyonun yeni çalışması https://turkpath.org.tr/files/pdf/rehber.pdf PBYS için önerilen özelliklere bakın. bu ise benim notlarımın bulunduğu sayfa https://www.parapathology.com/laboratory-management/laboratory-information-systems/patoloji-moduelue-oezellikleri zamanında ben bu şartnameyi hazırlamıştım. 2011 olmalı. O sırada kalite komisyonundaydım. Bir örneğini vermiştim komisyona. Çok da bir ilerleme kaydedememişler görünen o ki. Bari referans verselerdi.
https://bsky.app/profile/lucas.meyerperin.org/post/3lildqvlp4k2e
