Repositories list

• dive-dsa

  Public
  DIVE for Digital Slide Archive

  Vue

  •

  Apache License 2.0

  •0•1•9•7•Updated Sep 13, 2025Sep 13, 2025

• digital_slide_archive

  Public
  The official deployment of the Digital Slide Archive and HistomicsTK.

  hacktoberfesthistologybioimage-informatics+ 2digital-slide-archivehistomicstk

  Python

  •

  Apache License 2.0

  •57•127•30•0•Updated Sep 12, 2025Sep 12, 2025

• girder_volview

  Public
  Python

  •

  Other

  •3•3•10•1•Updated Sep 11, 2025Sep 11, 2025

• HistomicsUI

  Public
  A Girder plugin for pathology image annotations and analysis.

  pythonhistologydigital-slide-archive+ 1bioimage-infomatics

  JavaScript

  •

  Apache License 2.0

  •24•74•48•4•Updated Sep 11, 2025Sep 11, 2025

• ImageDePHI

  Public
  Python

  •

  Apache License 2.0

  •0•9•15•0•Updated Sep 11, 2025Sep 11, 2025

• HistomicsStream

  Public
  A whole-slide image reader for TensorFlow

  Python

  •

  Apache License 2.0

  •6•24•9•0•Updated Sep 8, 2025Sep 8, 2025

• HistomicsTK

  Public
  A Python toolkit for pathology image analysis algorithms.

  pythonmachine-learningcomputer-vision+ 4histologymedical-image-processingbioimage-informaticsdigital-slide-archive

  Python

  •

  Apache License 2.0

  •124•442•26•2•Updated Sep 8, 2025Sep 8, 2025

• girder-client-mount

  Public
  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Sep 8, 2025Sep 8, 2025

• superpixel-classification

  Public
  A test cli for classifying superpixels with arbitrary labels

  hacktoberfest

  Python

  •

  Other

  •4•5•0•4•Updated Sep 8, 2025Sep 8, 2025

• DSA-WSI-DeID

  Public
  A workflow for redacting PHI from whole slide images (WSI) based on the Digital Slide Archive.

  Python

  •

  Apache License 2.0

  •8•17•13•0•Updated Aug 18, 2025Aug 18, 2025

• girder-clamav

  Public
  Python

  •

  Other

  •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• histomics_aws_deployment

  Public
  Infrastructure-as-code scripts for deploying high-availability, scalable Histomics on AWS

  HCL

  •0•0•5•0•Updated Jul 22, 2025Jul 22, 2025

• large-image-utilities

  Public
  Experimental utilities for use with large_image

  Python

  •

  Apache License 2.0

  •1•4•0•0•Updated Jul 16, 2025Jul 16, 2025

• histomicstk-extras

  Public
  Python

  •

  Other

  •2•1•0•0•Updated Jul 16, 2025Jul 16, 2025

• histomicstk-similarity

  Public
  Identify similar tissue within an image using foundational models

  Python

  •

  Other

  •1•1•0•0•Updated Jul 11, 2025Jul 11, 2025

• tifftools

  Public
  Pure Python tools for reading and writing all TIFF IFDs, sub-IFDs, and tags.

  Python

  •

  Other

  •6•56•3•0•Updated Jul 10, 2025Jul 10, 2025

• histomics-label

  Public
  A user-interface used in conjunction with HistomicsUI to facilitate active learning on whole slide images

  pythonhistologybioimage-informatics+ 4digital-slide-archivewhole-slide-annotationwhole-slide-imagesguided-labeling

  Vue

  •

  Other

  •7•3•14•4•Updated Jun 20, 2025Jun 20, 2025

• girder_assetstore

  Public
  A Girder plugin for connecting remote Girder instances as Assetstores

  Python

  •

  Other

  •0•0•4•0•Updated Mar 5, 2025Mar 5, 2025

• import-tracker

  Public
  A Girder plugin for data import tracking in HistomicsUI

  Python

  •

  Other

  •3•2•7•1•Updated Nov 25, 2024Nov 25, 2024

• ALBench

  Public
  Benchmarking tool for evaluating Active Learning strategies for machine learning

  Python

  •

  Apache License 2.0

  •3•5•3•0•Updated Sep 4, 2024Sep 4, 2024

• histomics_load_testing

  Public
  HCL

  •

  Apache License 2.0

  •0•0•3•0•Updated Jul 18, 2024Jul 18, 2024

• annotation-tracker

  Public
  A Girder plugin for annotation tracking in HistomicsUI

  JavaScript

  •

  Other

  •0•4•2•2•Updated Feb 15, 2024Feb 15, 2024

• histoqc-dsa-plugin

  Public
  Python

  •2•1•3•0•Updated Feb 1, 2024Feb 1, 2024

• dsa-run-custom-ai-models

  Public
  Python

  •2•3•2•0•Updated Dec 15, 2023Dec 15, 2023

• histomics-tour

  Public
  Python

  •

  Other

  •0•0•0•2•Updated Aug 1, 2023Aug 1, 2023

• large_image_source_isyntax

  Public
  A large_image source using the Philips library for isyntax files

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Jun 16, 2023Jun 16, 2023

• HistomicsDetect

  Public
  A package for cell detection models using TensorFlow

  Python

  •

  Apache License 2.0

  •1•4•10•0•Updated Mar 20, 2023Mar 20, 2023

• CNNCellDetection

  Public
  This repository contains adaptations of the state-of-the-art deep learning based object detection models for the detection of cell nuclei in histology images

  Python

  •

  Apache License 2.0

  •3•26•0•22•Updated Dec 8, 2022Dec 8, 2022

• ImageDePHI-Phase-I

  Public
  Whole Slide Image Deidentification for PHI

  Python

  •

  Apache License 2.0

  •0•2•13•0•Updated Aug 27, 2021Aug 27, 2021

• HTAN

  Public
  Python

  •

  Other

  •1•0•4•0•Updated Jun 7, 2021Jun 7, 2021