BlenderProc2 — Peer-reviewed • Rank 23.2 • Science 100%

BlenderProc2: A Procedural Pipeline for Photorealistic Rendering - Published in JOSS (2023)

samgeo — Peer-reviewed • Rank 19.9 • Science 100%

samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM) - Published in JOSS (2023)

PlatiPy — Peer-reviewed • Rank 15.1 • Science 100%

PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python - Published in JOSS (2023)

SAMBA — Peer-reviewed • Rank 4.4 • Science 98%

SAMBA: A Trainable Segmentation Web-App with Smart Labelling - Published in JOSS (2024)

Annotate-Lab — Peer-reviewed • Rank 8.2 • Science 93%

Annotate-Lab: Simplifying Image Annotation - Published in JOSS (2024)

boxmot • Rank 22.4 • Science 77%

BoxMOT: Pluggable SOTA multi-object tracking modules modules for segmentation, object detection and pose estimation models

COVID-19 Lung Segmentation — Peer-reviewed • Rank 4.1 • Science 95%

COVID-19 Lung Segmentation - Published in JOSS (2021)

seg1d — Peer-reviewed • Rank 6.0 • Science 93%

seg1d: A Python package for Automated segmentation of one-dimensional (1D) data - Published in JOSS (2020)

pyransac3d • Rank 17.6 • Science 77%

A python tool for fitting primitives 3D shapes in point clouds using RANSAC algorithm

albumentations • Rank 30.2 • Science 59%

Fast and flexible image augmentation library. Paper about the library: https://www.mdpi.com/2078-2489/11/2/125

symbac • Rank 9.1 • Science 77%

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

labelfusion • Rank 7.0 • Science 77%

Implementation of various label fusion approaches for medical imaging.

monailabel • Rank 19.6 • Science 64%

MONAI Label is an intelligent open source image labeling and learning tool.

deepflash2 • Rank 5.7 • Science 77%

A deep-learning pipeline for segmentation of ambiguous microscopic images.

cellpose • Rank 22.8 • Science 59%

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

brainglobe-segmentation • Rank 12.5 • Science 67%

Segmentation of anatomical structures in a common coordinate space

orthoseg • Rank 11.4 • Science 67%

OrthoSeg makes it easy to train neural networks to segment orthophotos.

navis • Rank 15.4 • Science 59%

Python library for analysis of neuroanatomical data.

changepoint • Rank 19.0 • Science 54%

A place for the development version of the changepoint package on CRAN.

simpleitk • Rank 23.9 • Science 49%

SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.

mcmicro • Rank 5.6 • Science 67%

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

exllsm-circuit-reconstruction • Rank 4.3 • Science 67%

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

mapmos • Rank 5.8 • Science 65%

Building Volumetric Beliefs for Dynamic Environments Exploiting Map-Based Moving Object Segmentation (RAL 2023)

scikit-surgerytf • Rank 2.7 • Science 67%

Examples for running surgical segmentations using Tensor Flow

cam2bev • Rank 7.3 • Science 59%

TensorFlow Implementation for Computing a Semantically Segmented Bird's Eye View (BEV) Image Given the Images of Multiple Vehicle-Mounted Cameras.

geo-sam • Rank 7.0 • Science 59%

A QGIS plugin tool using Segment Anything Model (SAM) to accelerate segmenting or delineating landforms in geospatial raster images.

kelp-o-matic • Rank 11.0 • Science 54%

Segmentation Tools for Remotely Sensed RPAS Imagery

glasses-detector • Rank 15.9 • Science 49%

Glasses detection, classification and segmentation

tcd • Rank 5.7 • Science 59%

Restor's ML pipeline for tree crown mapping in aerial images

axondeepseg • Rank 15.0 • Science 49%

Axon/Myelin segmentation using Deep Learning

molkart • Rank 4.5 • Science 57%

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

@cornerstonejs/adapters • Rank 23.9 • Science 36%

Cornerstone is a set of JavaScript libraries that can be used to build web-based medical imaging applications. It provides a framework to build radiology applications such as the OHIF Viewer.

https://github.com/dipy/dipy • Rank 23.4 • Science 36%

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

fafbseg • Rank 9.8 • Science 49%

Tools to work with the FlyWire connectome. Fully interoperable with navis.

yeast-in-microstructures-dataset • Rank 3.7 • Science 54%

Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].

@stdlib/string-to-grapheme-cluster-iterator • Rank 8.6 • Science 44%

Create an iterator which iterates grapheme clusters.

taulu • Rank 8.4 • Science 44%

Taulu is a Python package designed to segment tabular data in scanned or photographed documents.

string-split-grapheme-clusters • Rank 8.0 • Science 44%

Split a string by its grapheme cluster breaks.

@stdlib/string-num-grapheme-clusters • Rank 6.8 • Science 44%

Return the number of grapheme clusters in a string.

pyspatialhistologyanalysis • Rank 1.1 • Science 49%

Package using StarDist and Python that performs object detection and spatial analysis on H&E images

https://github.com/ermshaua/claspy • Rank 11.1 • Science 36%

ClaSPy: A Python package for time series segmentation.

@stdlib/string-to-grapheme-cluster-iterator-right • Rank 2.3 • Science 44%

Create an iterator which iterates grapheme clusters.

s4a • Rank 5.8 • Science 39%

Sen4AgriNet: A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning

orca • Rank 0.0 • Science 44%

ORCA: Oceanic Recognition & Classification Application for sea-life analysis systems.

https://github.com/matrix-profile-foundation/matrixprofile • Rank 17.0 • Science 23%

A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms, accessible to everyone.

hagelslag • Rank 13.0 • Science 23%

Hagelslag supports segmentation and tracking of weather fields and scalable verification, including performance diagrams and reliability diagrams.

basketball_trainer • Rank 0.0 • Science 36%

:basketball: BasketballDetector training utilities

deepbrainseg • Rank 10.1 • Science 23%

Fully automatic brain tumour segmentation using Deep 3-D convolutional neural networks

digipathai • Rank 9.5 • Science 23%

Tool to visualize gigantic pathology images and use AI to segment cancer cells and present as an overlay

3d-forest • Rank 5.4 • Science 26%

Visualization, processing and analysis of Lidar point clouds, mainly focused on forest environment. New version of 3D Forest. Process files with terabytes of data. Edit new point attributes. Simple addition of new features by plugins.

rfm • Rank 13.4 • Science 13%

Customer Segmentation using RFM Analysis

machinevision-toolbox-matlab • Rank 5.4 • Science 18%

Machine Vision Toolbox for MATLAB

https://github.com/lromul/argus-tgs-salt • Rank 4.3 • Science 13%

Kaggle | 14th place solution for TGS Salt Identification Challenge

https://github.com/blutjens/eie-earth-public • Rank 3.2 • Science 13%

Official repo for 'Generating Physically-Consistent Satellite Imagery for Climate Visualizations'

https://github.com/catalyst-team/segmentation • Rank 5.1 • Science 10%

Catalyst.Segmentation

segmentation • Rank 2.3 • Science 10%

Boonelab segmentation for microscopy images

gt_structure_1_2 • Science 26%

The repo gt_structure_1_2 is part of the OCR-D Ground Truth Structure corpus. Only the structure of the printed page is annotated. The corpus was created as a result of the DFG project OCR-D.

gt_structure_1_4 • Science 26%

About The repo gt_structure_1_4 is part of the OCR-D Ground Truth Structure corpus. Only the structure of the printed page is annotated. The corpus was created as a result of the DFG project OCR-D.

https://github.com/omigutin/img_ops • Science 26%

Is a minimal, device‑aware image ops library built on top of OpenCV and NumPy.

sleeep • Science 26%

code, data and documentation behind the publication: Robustness Of Radiomics To Variations In Segmentation Methods In Multimodal Brain MRI

massmind • Science 57%

LWIR image segmentation dataset for maritime environment

mask-ukf • Science 67%

Instance Segmentation Aided 6D Object Pose and Velocity Tracking using an Unscented Kalman Filter

segment-anything-medical-evaluation • Science 41%

Code for "Segment Anything Model for Medical Image Analysis: an Experimental Study" in Medical Image Analysis

https://github.com/ai-forever/readingpipeline • Science 26%

Text reading pipeline that combines segmentation and OCR-models.

deepsleep2 • Science 49%

😴 DeepSleep2 is a compact U-Net-inspired convolutional neural network with 740,551 parameters, designed to predict non-apnea sleep arousals from full-length multi-channel polysomnographic recordings at 5-millisecond resolution. Achieves similar performance to DeepSleep with lower computational cost.

https://github.com/chris10m/vision-project-image-segmentation • Science 10%

slicer • Science 77%

Multi-platform, free open source software for visualization and image computing.

semantic-segmentation-of-landcover.ai-dataset • Science 67%

An implementation of Deeplabv3plus in TensorFlow2 for semantic land cover segmentation

multiscale-adversarial-attention-gates • Science 67%

Code for the paper: Valvano G. et al. (2021), Learning to Segment from Scribbles using Multi-scale Adversarial Attention Gates

detrex • Science 62%

detrex is a research platform for DETR-based object detection, segmentation, pose estimation and other visual recognition tasks.

4dmos • Science 62%

Receding Moving Object Segmentation in 3D LiDAR Data Using Sparse 4D Convolutions (RAL 2022)

https://github.com/brainlesion/panoptica • Science 36%

panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps

lsmquant • Science 57%

A pipeline for processing and analysis of light-sheet microscopy images.

sopa • Science 57%

Nextflow version of Sopa - spatial omics pipeline and analysis

gt_structure_1_3 • Science 26%

The repo gt_structure_1_3 is part of the OCR-D Ground Truth Structure corpus. Only the structure of the printed page is annotated. The corpus was created as a result of the DFG project OCR-D.

https://github.com/antsx/antsr • Science 59%

R interface to the ANTs biomedical image processing library

roft • Science 67%

Real-time Optical Flow-aided 6D Object Pose and Velocity Tracking

ssdf-nncore • Science 44%

nncore is a pytorch framework focusing on solving autonomous-driving problems.

spiers • Science 44%

SPIERS Software - Visualisation of tomographic data

https://github.com/bodenmillergroup/imcsegmentationpipeline • Science 36%

A pixel classification based multiplexed image segmentation pipeline

https://github.com/adaptivemotorcontrollab/cellseg3d • Science 59%

A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks

Lighter — Peer-reviewed • Science 93%

Lighter: Configuration-Driven Deep Learning - Published in JOSS (2025)

GIBBON — Peer-reviewed • Science 95%

GIBBON: The Geometry and Image-Based Bioengineering add-On - Published in JOSS (2018)

model_seg_mouse-sc_wm-gm_t1 • Science 67%

White and grey matter segmentation on T1-weighted exvivo mouse spinal cord

uni-vision • Science 44%

Python library for handling most vision tasks .\

prolesa-net-a-multi-channel-3d-architecture-for-prostate-mr-lesion-segmentation-with-multi-scale-ch • Science 49%

ProLesA-Net: a Deep learning model For Prostate Lesion Segmentation from bi-parametric MR-Images

pyhistology • Science 67%

Python package that uses colorspace-based segmentation to analyze histopathology images.

cnapse • Science 44%

Automated synapse detection in C. elegans EM images.

https://github.com/ai-forever/segm-model • Science 36%

An easy-to-run semantic segmentation model based on Unet

segmentation_gym • Science 77%

A neural gym for training deep learning models to carry out geoscientific image segmentation. Works best with labels generated using https://github.com/Doodleverse/dash_doodler

segmentator • Science 67%

3D MRI data exploration and segmentation tool.

https://github.com/cgre-aachen/bayseg • Science 23%

An unsupervised machine learning algorithm for the segmentation of spatial data sets.

https://github.com/chris10m/real-time-semantic-segmentation • Science 10%

wing-segmentation • Science 52%

Butterfly wing segmentation

2018-neon-beetles-processing • Science 75%

Processing code and exploratory notebooks for BeetlePalooza dataset (2018 NEON Ethanol-preserved Ground Beetles).

string-num-code-points • Science 44%

Return the number of code points in a string.

ocr17plus • Science 26%

Data for layout analysis and HTR.

@stdlib/string-next-code-point-index • Science 44%

Return the position of the next Unicode code point in a string after a specified position.

cataloguessegmentationocr • Science 26%

Dataset and models for catalogs' Layout analysis and HTR

lasermix • Science 54%

[CVPR 2023 Highlight] LaserMix for Semi-Supervised LiDAR Semantic Segmentation