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bioptort

A tool for measuring tortuosity in biopsy samples

cohortfinder

Intelligent data partitioning using quality control metrics

dicom2tiff

Conversion of DICOM-WSI directories to OpenSlide compatible pyramidal TIFF files

featureanalysis

Data exploration of features in DP

histoblur

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

histoqc

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

hoverfast

Blazing fast nuclei segmentation for brightfield Whole Slide Images

icav-pr

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

loopicide

A simple algorithm for removing spatial loops in ordered point arrays without using a graph-based approach like Dijkstra's algorithm.

patchsorter

A tool for rapidly labeling objects using deep learning feature embedding

public

pytorchdigitalpathology

An implementation of Unet for pytorch designed for digital pathology segmentation

qcsliderepo-web

The simple Flask based web repository for HistoQC.

quickannotator

An open-source digital pathology based rapid image annotation tool

quickreviewer

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

qupathgeojsonimportexport

Coincides with blogpost for using geojson and shapely

qupathpaquointegration

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

qupaththreshold

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

rayblogpost

snippets

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

tortugrade

A tool for measuring tortuosity in biopsy samples

traithorizon

a plotly based feature reviewing UI