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The Top 21 Bioimage Analysis Open Source Projects

Open source projects categorized as Bioimage Analysis
Categories > Bioimage Analysis
Qupath ⭐ 934
QuPath - Bioimage analysis & digital pathology
most recent commit 5 months ago
Stardist ⭐ 788
StarDist - Object Detection with Star-convex Shapes
dependent packages 22total releases 29most recent commit 5 months agopypi stardist} Downloads
Pyclesperanto_prototype ⭐ 173
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
dependent packages 13total releases 69most recent commit 6 months agopypi pyclesperanto-prototype} Downloads
Toad ⭐ 94
AI-based pathology predicts origins for cancers of unknown primary - Nature
most recent commit 3 years ago
Python For Bioimage Analysis ⭐ 86
This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.
most recent commit 4 years ago
Plant Seg ⭐ 81
A tool for cell instance aware segmentation in densely packed 3D volumetric images
most recent commit 5 months ago
Awesome Biological Image Analysis ⭐ 74
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
most recent commit 5 months ago
Sish ⭐ 72
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
most recent commit a year ago
Mastodon ⭐ 61
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
most recent commit 3 months ago
Deepflash2 ⭐ 49
A deep-learning pipeline for segmentation of ambiguous microscopic images.
dependent packages 1total releases 27most recent commit a year agopypi deepflash2} Downloads
Pi2 ⭐ 41
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
most recent commit a year ago
Multitemplatematching Fiji ⭐ 34
Fiji plugin for object(s) detection using template(s) matching
most recent commit 5 months ago
Partseg ⭐ 28
Tool for segmentation in bioimaging
dependent packages 4total releases 75most recent commit 5 months agopypi PartSeg} Downloads
Imagej_macros_and_scripts ⭐ 26
ImageJ macros and scripts written at the imaging facility MRI
most recent commit 5 months ago
Simpli ⭐ 24
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
most recent commit a year ago
Tysserand ⭐ 22
Fast reconstruction of spatial networks from bioimages.
total releases 6most recent commit 7 months ago
Magellanmapper ⭐ 18
MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
total releases 2most recent commit 5 months ago
Core Bioimage Io Python ⭐ 13
Python libraries for loading, running and packaging bioimage.io models
dependent packages 7total releases 33most recent commit 6 months agopypi bioimageio.core} Downloads
Pcnadeep ⭐ 9
Track single cells and profile the cell cycle with PCNA fluorescence images
most recent commit 10 months ago
Viscy ⭐ 6
computer vision models for single-cell phenotyping
most recent commit 6 months ago
Scip ⭐ 5
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.
most recent commit a year ago
The 5 Most Depended On Bioimage Analysis Open Source Projects
Stardist ⭐ 788
StarDist - Object Detection with Star-convex Shapes
dependent packages 22total releases 29latest release July 21, 2023most recent commit 5 months agopypi stardist} Downloads
Pyclesperanto_prototype ⭐ 173
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
dependent packages 13total releases 69latest release January 15, 2023most recent commit 6 months agopypi pyclesperanto-prototype} Downloads
Core Bioimage Io Python ⭐ 13
Python libraries for loading, running and packaging bioimage.io models
dependent packages 7total releases 33latest release November 15, 2023most recent commit 6 months agopypi bioimageio.core} Downloads
Partseg ⭐ 28
Tool for segmentation in bioimaging
dependent packages 4total releases 75latest release August 28, 2023most recent commit 5 months agopypi PartSeg} Downloads
Deepflash2 ⭐ 49
A deep-learning pipeline for segmentation of ambiguous microscopic images.
dependent packages 1total releases 27latest release July 16, 2022most recent commit a year agopypi deepflash2} Downloads
The 7 Latest Releases In Bioimage Analysis Open Source Projects
Core Bioimage Io Python ⭐ 13
Python libraries for loading, running and packaging bioimage.io models
dependent packages 7total releases 33latest release November 15, 2023most recent commit 6 months agopypi bioimageio.core} Downloads
Partseg ⭐ 28
Tool for segmentation in bioimaging
dependent packages 4total releases 75latest release August 28, 2023most recent commit 5 months agopypi PartSeg} Downloads
Stardist ⭐ 788
StarDist - Object Detection with Star-convex Shapes
dependent packages 22total releases 29latest release July 21, 2023most recent commit 5 months agopypi stardist} Downloads
Pyclesperanto_prototype ⭐ 173
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
dependent packages 13total releases 69latest release January 15, 2023most recent commit 6 months agopypi pyclesperanto-prototype} Downloads
Deepflash2 ⭐ 49
A deep-learning pipeline for segmentation of ambiguous microscopic images.
dependent packages 1total releases 27latest release July 16, 2022most recent commit a year agopypi deepflash2} Downloads
Tysserand ⭐ 22
Fast reconstruction of spatial networks from bioimages.
total releases 6latest release November 17, 2021most recent commit 7 months ago
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