PAthological QUpath Obsession - QuPath and Python conversations
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Apr 30, 2026 - Python
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qupath
Here are 48 public repositories matching this topic...
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.
python opencv machine-learning gui javafx pytorch unet-image-segmentation qupath deep-java-library gel-electrophoresis gel-segmentation
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Jul 13, 2025 - Python
🔬 Code-free deep segmentation for computational pathology
java deep-learning annotation cpp matlab medical-imaging convolutional-neural-networks semantic-segmentation digital-pathology open-datasets multi-class u-net qupath fastpathology deepmib open-annotations
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Jun 14, 2024 - Jupyter Notebook
Toolkit to help develop and run QuPath scripts from Eclipse and other IDEs, including over remote connections. (See README.md for more information)
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Aug 19, 2020 - Groovy
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.
gtk cross-platform imagej geojson biology plugins bio-formats omero roi microscopy openslide image-stacks qupath whole-slide-image imagej-roi imagej-tiff segment-anything segment-anything-model sam-2
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Jul 18, 2026 - C#
🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
machine-learning dicom medical-imaging atlas typer pydicom openslide digital-pathology whole-slide-imaging uv pydantic qupath nicegui marimo oe-python-template aignostics image-data-commons
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Sep 5, 2026 - Python
pipeline that converts Deepcell generated instance segmentation masks of nuclei from an ome-tiff to Cell Objects with auto-generated cytoplasms in QuPath
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Apr 26, 2025 - Jupyter Notebook
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
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Apr 19, 2024 - Groovy
Intel OpenVINO extension for QuPath, a digital pathology platform
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Dec 7, 2022 - Java
Materials supporting the QuPath workshop at Harvard Medical School.
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Feb 10, 2025
A collection of groovy scripts for digital pathology
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Nov 6, 2024 - Groovy
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.
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Jul 19, 2026 - C#
An image analysis pipeline for quantifying the spatial distribution of cell markers in stroma-rich tumors
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Sep 18, 2024 - Jupyter Notebook
Converting GeoJSON annotations from QuPath to COCO style.
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Aug 27, 2023 - Python
QuPath BioCampus workshop proposed by MRI
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Jun 4, 2026 - Jupyter Notebook
QuIET - QuPath Image Export Toolkit: batch export images for publication or model training
machine-learning microscopy bioimage-analysis qupath image-export publication-figures qupath-extension quarep-limi
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Aug 20, 2026 - Java
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