BlenderProc2
BlenderProc2: A Procedural Pipeline for Photorealistic Rendering - Published in JOSS (2023)
samgeo
samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM) - Published in JOSS (2023)
PlatiPy
PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python - Published in JOSS (2023)
SAMBA
SAMBA: A Trainable Segmentation Web-App with Smart Labelling - Published in JOSS (2024)
Annotate-Lab
Annotate-Lab: Simplifying Image Annotation - Published in JOSS (2024)
boxmot
BoxMOT: Pluggable SOTA multi-object tracking modules modules for segmentation, object detection and pose estimation models
COVID-19 Lung Segmentation
COVID-19 Lung Segmentation - Published in JOSS (2021)
seg1d
seg1d: A Python package for Automated segmentation of one-dimensional (1D) data - Published in JOSS (2020)
pyransac3d
A python tool for fitting primitives 3D shapes in point clouds using RANSAC algorithm
albumentations
Fast and flexible image augmentation library. Paper about the library: https://www.mdpi.com/2078-2489/11/2/125
symbac
Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
labelfusion
Implementation of various label fusion approaches for medical imaging.
monailabel
MONAI Label is an intelligent open source image labeling and learning tool.
deepflash2
A deep-learning pipeline for segmentation of ambiguous microscopic images.
cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
brainglobe-segmentation
Segmentation of anatomical structures in a common coordinate space
orthoseg
OrthoSeg makes it easy to train neural networks to segment orthophotos.
changepoint
A place for the development version of the changepoint package on CRAN.
simpleitk
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
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
exllsm-circuit-reconstruction
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery
mapmos
Building Volumetric Beliefs for Dynamic Environments Exploiting Map-Based Moving Object Segmentation (RAL 2023)
scikit-surgerytf
Examples for running surgical segmentations using Tensor Flow
cam2bev
TensorFlow Implementation for Computing a Semantically Segmented Bird's Eye View (BEV) Image Given the Images of Multiple Vehicle-Mounted Cameras.
geo-sam
A QGIS plugin tool using Segment Anything Model (SAM) to accelerate segmenting or delineating landforms in geospatial raster images.
molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
@cornerstonejs/adapters
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
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
Tools to work with the FlyWire connectome. Fully interoperable with navis.
yeast-in-microstructures-dataset
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
taulu
Taulu is a Python package designed to segment tabular data in scanned or photographed documents.
pyspatialhistologyanalysis
Package using StarDist and Python that performs object detection and spatial analysis on H&E images
https://github.com/ermshaua/claspy
ClaSPy: A Python package for time series segmentation.
s4a
Sen4AgriNet: A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning
orca
ORCA: Oceanic Recognition & Classification Application for sea-life analysis systems.
https://github.com/matrix-profile-foundation/matrixprofile
A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms, accessible to everyone.
hagelslag
Hagelslag supports segmentation and tracking of weather fields and scalable verification, including performance diagrams and reliability diagrams.
deepbrainseg
Fully automatic brain tumour segmentation using Deep 3-D convolutional neural networks
digipathai
Tool to visualize gigantic pathology images and use AI to segment cancer cells and present as an overlay
3d-forest
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.
https://github.com/lromul/argus-tgs-salt
Kaggle | 14th place solution for TGS Salt Identification Challenge
https://github.com/blutjens/eie-earth-public
Official repo for 'Generating Physically-Consistent Satellite Imagery for Climate Visualizations'
ailcap
An implementation of deep learning segmentation models in digital pathology field
mask-ukf
Instance Segmentation Aided 6D Object Pose and Velocity Tracking using an Unscented Kalman Filter
rrwnet
Official repository of the paper "RRWNet: Recursive Refinement Network for Effective Retinal Artery/Vein Segmentation and Classification", published in Expert Systems with Applications (Dec 2024).
segmentation_gym
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
https://github.com/christophreich1996/oss-net
Official and maintained implementation of the paper "OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data" [BMVC 2021].
magms
Modality-Agnostic Learning for Medical Image Segmentation Using Multi-modality Self-distillation
dacapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
https://github.com/cbica/brainmage
Brain extraction in presence of abnormalities, using single and multiple MRI modalities
https://github.com/bamresearch/automatic-sem-image-segmentation
Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images
https://github.com/cyberagentailab/sprite-decompose
Fast Sprite Decomposition from Animated Graphics [ECCV2024]
https://github.com/arbit3rr/unet-aerialsegmentation
A PyTorch implementation of U-Net for aerial imagery semantic segmentation.
https://github.com/antsx/antsr
R interface to the ANTs biomedical image processing library
ssdf-nncore
nncore is a pytorch framework focusing on solving autonomous-driving problems.
pituitary-segmentation-tool
This repository contains code that normalizes head MRIs segments the pituitary gland.
https://github.com/brainlesion/aurora
Segmentation models for cancer metastasis in brain MR
scribbleprompt
[ECCV 2024] ScribblePrompt: Fast and Flexible Interactive Segmentation for Any Medical Image
ple
[IROS 2024] Learning from Spatio-temporal Correlation for Semi-Supervised LiDAR Semantic Segmentation
gt_structure_1_2
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.
slicer
Multi-platform, free open source software for visualization and image computing.
gt_structure_1_1
The repo gt_structure_1_1 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/bodenmillergroup/imcsegmentationpipeline
A pixel classification based multiplexed image segmentation pipeline
gandlf
A generalizable application framework for segmentation, regression, and classification using PyTorch
https://github.com/adaptivemotorcontrollab/cellseg3d
A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks
2018-neon-beetles-processing
Processing code and exploratory notebooks for BeetlePalooza dataset (2018 NEON Ethanol-preserved Ground Beetles).
GIBBON
GIBBON: The Geometry and Image-Based Bioengineering add-On - Published in JOSS (2018)
magic-portrait
Magic Portrait is an android application for transforming the style of a pet in an image to a desired style.
https://github.com/connectomicslab/aneurysm_detection
This repository contains the code used for the paper "Towards automated brain aneurysm detection in TOF-MRA: open data, weak labels, and anatomical knowledge "
prolesa-net-a-multi-channel-3d-architecture-for-prostate-mr-lesion-segmentation-with-multi-scale-ch
ProLesA-Net: a Deep learning model For Prostate Lesion Segmentation from bi-parametric MR-Images
gt_structure_1_4
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.
covid-19-detection
Covid-19 Detection using Computer Vision, Machine Learning and Deep Learning
deepsleep2
😴 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/brainlesion/stroke_segmentor
stroke segmentation in MRI data
semantic-segmentation-of-landcover.ai-dataset
An implementation of Deeplabv3plus in TensorFlow2 for semantic land cover segmentation
https://github.com/brainlesion/deep_quality_estimation
Quality estimation for BraTS glioma segmentation models