A tool for cell instance aware segmentation in densely packed 3D volumetric images
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Updated
May 25, 2024 - Python
A tool for cell instance aware segmentation in densely packed 3D volumetric images
QuPath - Bioimage analysis & digital pathology
MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
Python libraries for loading, running and packaging bioimage.io models
computer vision models for single-cell phenotyping
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
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
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.
A vision-language foundation model for computational pathology - Nature Medicine
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