Pinned Repositories
CohortFinder
Intelligent data partitioning using quality control metrics
HistoQC
HistoQC is an open-source quality control tool for digital pathology slides
HoverFast
Blazing fast nuclei segmentation for brightfield Whole Slide Images
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
QuickAnnotator
An open-source digital pathology based rapid image annotation tool
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
Snippets
Pieces of code likely to be useful as part of larger projects
choosehappy's Repositories
choosehappy/HistoQC
HistoQC is an open-source quality control tool for digital pathology slides
choosehappy/PytorchDigitalPathology
An implementation of Unet for pytorch designed for digital pathology segmentation
choosehappy/public
choosehappy/QuickAnnotator
An open-source digital pathology based rapid image annotation tool
choosehappy/HoverFast
Blazing fast nuclei segmentation for brightfield Whole Slide Images
choosehappy/QuPathGeoJSONImportExport
Coincides with blogpost for using geojson and shapely
choosehappy/PatchSorter
A tool for rapidly labeling objects using deep learning feature embedding
choosehappy/Snippets
Pieces of code likely to be useful as part of larger projects
choosehappy/CohortFinder
Intelligent data partitioning using quality control metrics
choosehappy/QuPathPaquoIntegration
Code for the blogpost showing how to use Paquo to interact with, and classify, objects in QuPath with machine learning
choosehappy/HistoBlur
A tool for building an annotation free blur detector for digital pathology slides
choosehappy/QuickReviewer
Allows for multiple people to quickly review images and provide categorical feedback
choosehappy/iCAV-Pr
Code for the Circulation paper: "Computational Analysis of Routine Biopsies Improves Diagnosis and Prediction of Cardiac Allograft Vasculopathy" 2022
choosehappy/QuPathThreshold
A repo for the blog post discussing how to use qupath to identify ideal thresholds
choosehappy/BiopTort
A tool for measuring tortuosity in biopsy samples
choosehappy/dicom2tiff
Conversion of DICOM-WSI directories to OpenSlide compatible pyramidal TIFF files
choosehappy/FeatureAnalysis
Data exploration of features in DP
choosehappy/loopicide
A simple algorithm for removing spatial loops in ordered point arrays without using a graph-based approach like Dijkstra's algorithm.
choosehappy/qcsliderepo-web
The simple Flask based web repository for HistoQC.
choosehappy/RayBlogpost
choosehappy/TortuGrade
A tool for measuring tortuosity in biopsy samples
choosehappy/TraitHorizon
a plotly based feature reviewing UI