PAthological QUpath Obsession - QuPath and Python conversations

🔬 Code-free deep segmentation for computational pathology

Toolkit to help develop and run QuPath scripts from Eclipse and other IDEs, including over remote connections. (See README.md for more information)

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Intel OpenVINO extension for QuPath, a digital pathology platform

MarrowQuant is a user-friendly algorithm for the quantification of H&E bone marrow tissue biopsies in whole slide images, implemented as a series of QuPath Scripts. Keywords: Digital Pathology, Whole slide Imaging, QuPath, Bone Marrow, Adiposity

A collection of groovy scripts for digital pathology

Supplementary information associated with Besson et al. (2019) ECDP 2019

pipeline that converts Deepcell generated instance segmentation masks of nuclei from an ome-tiff to Cell Objects with auto-generated cytoplasms in QuPath

A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.

Cartilage analysis for Toluidine blue slides

DRUGSENS is a R-package that allows users to automatically analyze QuPath™ output data from imaging analysis

Custom groovy scripts for QuaPath

nuclei segmentation by treshold, watershed methods & stardist neural network (educational project)

Converting GeoJSON annotations from QuPath to COCO style.

Script for semi-automated bone volume quantification on Fast green Slides