List of Projects

Flat index of every repository under ~/Documents/GitHub, grouped by cluster

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A flat, searchable index of everything under the group’s GitHub organization and local ~/Documents/GitHub directory. For guidance on which of these you should start with, see the Onboarding page.

Flagship / jamovi modules

Digital pathology / WSI tooling

  • Viewers: DIYWSI, simple_wsi_viewer, slide_viewer_47, video-wsi, imageTypes.
  • PACS: sectra-qupath-extension, sectra-python-qupath-extension.
  • QC: HistoQC, grandQC_quality_study, PathProfiler, CohortFinder, TissueSelector.
  • Annotation / DL: QuickAnnotator, HistomicsML, pathology-hooknet, paige-prostate, aiforiabreast, tiatoolbox, pathml, pathml-tutorial, DL4MicEverywhere.
  • Interfaces: morphology-ai-research-liver-interface, morphology-research-pancreas-interface.
  • Operational: scan-time-in-real-life.

Clinical case studies and cohorts

Pancreas / GI: PDAC-adrenal-invasion, PDAC-benign-vs-malignant, PDAC-cytology, PDAC_LN_shell, pdac-large-duct, pancreas-adenosquamous, pancreas-solid-pseudopapillary, ampullary-adenocarcinoma, ectopic-pancreas, duodenum-tubular-adenoma, lymphocytic-gastritis, sarcina-ventriculi, eosinophilic-esophagitis, acute-perforated-appendicitis, omentum, liver-transplant-acute-rejection.

Breast: breast-lobular-carcinoma, HER2-intratumoral-heterogeneity, CSF-breast-carcinoma-metastasis.

CNS: CNS, WHO-CNS, glioblastoma, secretory-meningioma, arachnoid-cyst, pilocytic-astrocytoma, ganglioneuroma, CSF-metastasis.

GU / thoracic / colorectal: onc_rcc, oncotype, lung-squamous-cell-carcinoma, extramural-venous-invasion-elastic (ekstramural-venoz-inv-elastik), pathology-report-colon-QA.

Other: morphea, trypsin, fistula, rokitansky-aschoff-sinus, serous-carcinoma-psammoma-bodies, parasite, trps1, gpnmb, PASAB, MIA, LOP, EO1, ekrapor, ekrapor-oncalisma.

Report text, NLP, AI skills

  • extract-report-text, pathology-reports-text-analysis, pathology-report-colon-QA, pathology-report-checker-skill.
  • pathology-skills-collection, claude-scientific-skills.
  • n8n-pathology, pathology_atlas_pipeline.
  • bibliometrics, markitdown, repo2file.

Public sites and communication

  • sbalci.github.io, drozlembalci.github.io, MemorialPath.github.io, patolojiatlasi.github.io, whowriteswho.github.io.
  • research (this portal).
  • patoloji-hakkinda, patoloji-ve-bilisim, patolojirapor, patolojiraporlari, rutinde-dijital-patoloji, patoloji-bilgi-yonetim-sistemi.
  • konsultasyon, ASDP-podcast, BlueSky.

Templates and utilities

  • Scaffolds: template, histopathology-template, seed.
  • R utilities: MyRCodesForDataAnalysis, histopatoloji-calismalarinda-biyoistatistik-icin-veri-hazirlama, clinicopathological, JamoviTest, SimpleTests, Rj, RwithFileMaker, vtree.
  • Data / deployment: pathologyAnonymData, shiny-server, intranet, local, data.
  • Misc: qrcodes, TODO, PembeBobrek, PinkKidney, ParaPathology, quality-feedback.

Archived teaching

  • EAS1 … EAS29.
  • ClinicoPathLinuxDescriptives, MemorialPathStats.

This list is intentionally flat. For task-first guidance (which repo to open for which kind of work), see Onboarding.

In the research wiki

  • Wiki — Front Door — the wiki’s own front door, which lists the same estate by what each repository is for rather than by folder, with a one-line summary per page and a Known gaps section.
  • QuPath Tooling — the digital-pathology cluster as a single curated index with a verdict per repository.
  • ClinicoPath Org Collection — the jamovi cluster’s organisation-level catalogue.
  • Digital Pathology Drafts — the umbrella the prototype repositories sit inside, and the page to read before cloning any of them.
  • Aknar–Mutlu Model Family — the only project in the estate that sets out to train an encoder rather than download one — OpenMidnight LoRA-adapted to a Turkish multi-organ cohort.
  • Meningioma H&E Deep Learning — reproducing a published model that predicts methylation-defined molecular groups from H&E alone, which would substitute a slide the department already has for an assay it does not run.
  • PinkKidneyWeb — the deploy-mirror pattern in miniature: content written in one repository, analysed in a second, published from a third.