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.

Open-Source package for segmentation and analysis of gel electrophoresis images using machine learning. Both a python framework for training/running models and a QuPath GUI extension are available.

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

Materials supporting the QuPath workshop at Harvard Medical School.

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

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

Converting GeoJSON annotations from QuPath to COCO style.

Custom groovy scripts for QuaPath

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

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

An image analysis pipeline for quantifying the spatial distribution of cell markers in stroma-rich tumors