QuPath - Bioimage analysis & digital pathology
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Updated
May 30, 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.
Python libraries for loading, running and packaging bioimage.io models
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
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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