A tool for cell instance aware segmentation in densely packed 3D volumetric images
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Updated
Jun 1, 2024 - Python
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
A Jupyter notebook to identify collective cell signalling in raw microscopy images
MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
computer vision models for single-cell phenotyping
QuPath - Bioimage analysis & digital pathology
Python libraries for loading, running and packaging bioimage.io models
Scalable Cytometry Image Processing (SCIP) is an open-source tool that implements an image processing pipeline on top of Dask, a distributed computing framework written in Python. SCIP performs projection, illumination correction, image segmentation and masking, and feature extraction.
ImageJ macros and scripts written at the imaging facility MRI
Evaluation of label free cell and nuclei segmentation
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
U-Net implementation in PyTorch for segmentation of bio-images
Main repository gathering all content of the EMBO-DL4MIA 2024 course.
Automated batch processing for tissue microscopy image data
Fast reconstruction of spatial networks from bioimages.
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
Benchmarking Large Language Models for Bio-Image Analysis Code Generation
StarDist - Object Detection with Star-convex Shapes
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
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