bioimage-analysis
There are 6 repositories under bioimage-analysis topic.
- Language:Java 995
- stardistLanguage:Python 849
- pyclesperanto_prototype
clEsperanto / pyclesperanto_prototype
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
Language:Jupyter Notebook 200 mahmoodlab / CONCH
A vision-language foundation model for computational pathology - Nature Medicine
Language:Python 182AI-based pathology predicts origins for cancers of unknown primary - Nature
Language:Python 167RMS-DAIM / Python-for-Bioimage-Analysis
This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.
Language:Jupyter Notebook 129- awesome-biological-image-analysis
hallvaaw / awesome-biological-image-analysis
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
Language:Python 93kreshuklab / plant-seg
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Language:Python 87- mastodon
mastodon-sc / mastodon
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
Language:Java 65 matjesg / deepflash2
A deep-learning pipeline for segmentation of ambiguous microscopic images.
Language:Jupyter Notebook 56arttumiettinen / pi2
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
Language:C++ 48- MultiTemplateMatching-Fiji
multi-template-matching / MultiTemplateMatching-Fiji
Fiji plugin for object(s) detection using template(s) matching
Language:Python 35 ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
Language:R 33- imagej_macros_and_scripts
MontpellierRessourcesImagerie / imagej_macros_and_scripts
ImageJ macros and scripts written at the imaging facility MRI
Language:ImageJ Macro 29 - PartSegLanguage:Python 28
VeraPancaldiLab / tysserand
Fast reconstruction of spatial networks from bioimages.
Language:Python 24bioimage-io / core-bioimage-io-python
Python libraries for loading, running and packaging bioimage.io models
Language:Jupyter Notebook 21- Language:Python 20
sanderslab / magellanmapper
MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
Language:Python 20Guides and code for 3D nuclear instance segmentation
Language:Python 16chan-labsite / PCNAdeep
Track single cells and profile the cell cycle with PCNA fluorescence images
Language:Python 10haesleinhuepf / human-eval-bia
Benchmarking Large Language Models for Bio-Image Analysis Code Generation
Language:Jupyter Notebook 8- SCIP
ScalableCytometryImageProcessing / SCIP
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.
Language:Python 7 - Language:Jupyter Notebook 6
psobolewskiPhD / napari_scripts
Collection of useful (to me) python scripts for interacting with napari
Language:Python 6WhoIsJack / tissue_exploder
Create a nice exploded visualization of segmented cells in a tissue.
Language:Python 5- Language:C++ 4
MercaderLabAnatomy / T-MIDAS
Automated batch processing for tissue microscopy image data
Language:Cool 3- Language:Jupyter Notebook 3
SOCR / 3d-cell-morphometry
Source code and workflow protocols for SOCR 3D Cell Morphometry Project
Language:C 3- Language:C++ 3
Visualise pcnaDeep single-cell tracking data
Language:Python 2dl4mia / DL4MIA_2024
Main repository gathering all content of the EMBO-DL4MIA 2024 course.
Language:Shell 2Euro-BioImaging / OME_Zarr_Tools
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
Language:Shell 2FabrizioMusacchio / Napari_Bioimage_Analysis
Image data and Python scripts for the course on Bioimage analysis with Napari
Language:Python 2
