BIOP/qupath-extension-cellpose

an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

Language: Jupyter Notebook - Size: 3.08 MB - Last synced at: about 13 hours ago - Pushed at: about 14 hours ago - Stars: 72 - Forks: 13

aignostics/python-sdk

🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.

Language: Python - Size: 55.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 6 - Forks: 0

BiologyTools/BioGTK

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.

Language: C# - Size: 146 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 14 - Forks: 2

BIOP/qupath-extension-biop-omero Fork of qupath/qupath-extension-omero-web

QuPath extension to work with images through OMERO's Java API (raw)

Language: Java - Size: 2.02 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 5 - Forks: 1

flalom/drugsens

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

Language: R - Size: 1.6 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

sbalci/sectra-qupath

Using Sectra PACS Annotations in QuPath

Language: Groovy - Size: 37.1 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

mattaq31/GelGenie

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.

Language: Python - Size: 158 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 51 - Forks: 4

SPerrott22/Deepcell-to-QuPath

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

Language: Jupyter Notebook - Size: 37 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 0

Bayer-Group/paquo

PAthological QUpath Obsession - QuPath and Python conversations

Language: Python - Size: 839 KB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 115 - Forks: 18

HMS-IAC/qupath-workshop

Materials supporting the QuPath workshop at Harvard Medical School.

Size: 90.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 1

BiologyTools/BioLib

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.

Language: C# - Size: 65.2 MB - Last synced at: 11 days ago - Pushed at: 5 months ago - Stars: 3 - Forks: 1

andreped/NoCodeSeg

🔬 Code-free deep segmentation for computational pathology

Language: Jupyter Notebook - Size: 11.2 MB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 53 - Forks: 17

dkurt/qupath-extension-openvino

Intel OpenVINO extension for QuPath, a digital pathology platform

Language: Java - Size: 89.8 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

openmicroanatomy/qupath-edu-extension

Language: Java - Size: 937 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 2

elijahedmondson/QuPath-scripts

A collection of groovy scripts for digital pathology

Language: Groovy - Size: 105 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 1

Naveiras-Lab/MarrowQuant

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

Language: Groovy - Size: 28.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 1

MohamedOmar2020/QuPath_scripts

Custom groovy scripts for QuaPath

Language: Groovy - Size: 8.79 KB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ibrahimberb/QuGeoCOCO

Converting GeoJSON annotations from QuPath to COCO style.

Language: Python - Size: 1.23 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

ome/ecdp2019-publication

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

Language: Python - Size: 6.43 MB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 3

ChristelleSanchez/Bone_volume_SFG

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

Language: Groovy - Size: 970 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

ChristelleSanchez/Cartilage_Toluidineblue

Cartilage analysis for Toluidine blue slides

Language: Groovy - Size: 9.1 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

arjvik/QuPath-Scripting-Tools

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

Language: Groovy - Size: 173 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 15 - Forks: 1