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HistoQC. HistoQC is an open-source quality control tool for digital pathology slides

PytorchDigitalPathology. An implementation of Unet for pytorch designed for digital pathology segmentation

QuickAnnotator. An open-source digital pathology based rapid image annotation tool

public. Jupyter Notebook

HoverFast. Blazing fast nuclei segmentation for brightfield Whole Slide Images

PatchSorter. A tool for rapidly labeling objects using deep learning feature embedding

QuPathGeoJSONImportExport. Coincides with blogpost for using geojson and shapely

Snippets. Pieces of code likely to be useful as part of larger projects

CohortFinder. Intelligent data partitioning using quality control metrics

QuPathPaquoIntegration. Code for the blogpost showing how to use Paquo to interact with, and classify, objects in QuPath with machine learning

HistoBlur. A tool for building an annotation free blur detector for digital pathology slides

QuickReviewer. Allows for multiple people to quickly review images and provide categorical feedback

QuPathThreshold. A repo for the blog post discussing how to use qupath to identify ideal thresholds

iCAV-Pr. Code for the Circulation paper: "Computational Analysis of Routine Biopsies Improves Diagnosis and Prediction of Cardiac Allograft Vasculopathy" 2022

BiopTort. A tool for measuring tortuosity in biopsy samples