QuPath - Bioimage analysis & digital pathology
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Updated
May 20, 2024 - Java
QuPath - Bioimage analysis & digital pathology
StarDist - Object Detection with Star-convex Shapes
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
AI-based pathology predicts origins for cancers of unknown primary - Nature
This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
Python libraries for loading, running and packaging bioimage.io models
ImageJ macros and scripts written at the imaging facility MRI
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
A vision-language foundation model for computational pathology - Nature Medicine
A deep-learning pipeline for segmentation of ambiguous microscopic images.
Fiji plugin for object(s) detection using template(s) matching
Fast reconstruction of spatial networks from bioimages.
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
Evaluation of label free cell and nuclei segmentation
Collection of useful (to me) python scripts for interacting with napari
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