cell-segmentation
There are 121 repositories under cell-segmentation topic.
MouseLand/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
qupath/qupath
QuPath - Open-source bioimage analysis for research
stardist/stardist
StarDist - Object Detection with Star-convex Shapes
computational-cell-analytics/micro-sam
Segment Anything for Microscopy
TissueImageAnalytics/tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
aristoteleo/spateo-release
Spatiotemporal modeling of spatial transcriptomics
nadeemlab/DeepLIIF
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
oist/Usiigaci
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
yaoguangluo/ETL_Unicorn
数据可视化, 数据挖掘, 数据处理 ETL分析
Lee-Gihun/MEDIAR
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
FZJ-INM1-BDA/celldetection
Scalable Instance Segmentation using PyTorch & PyTorch Lightning.
amirhossein-kz/HiFormer
HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)
royerlab/ultrack
Cell tracking and segmentation software
ChristophReich1996/Cell-DETR
Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].
mkang315/ASF-YOLO
[IMAVIS] Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".
okunator/cellseg_models.pytorch
Encoder-Decoder Cell and Nuclei segmentation models
EliHei2/segger_dev
a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).
Omid-Nejati/BEFUnet
A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation
marshuang80/cell-segmentation
PyTorch implementation of several neural network models for cellular image segmentation
wanglab-broad/ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
nadeemlab/ImPartial
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
stardist/stardist-napari
StarDist plugin for napari
ciccalab/SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
SAIL-GuoLab/Cell_Segmentation_and_Tracking
For cell segmentation and tracking.
KevinCortacero/Kartezio
Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming
iitmcvg/Cell-Segmentation
Automated identification of cell boundaries from the pathological video data
Mmasoud1/HistoJS
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
ariel-waisman/LabelsToROIs
A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
DanuserLab/u-segment3D
Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.
kdha0727/cancer-instance-segmentation-from-tissue
Tissue Cancer Segmentation project using multiple segmentation networks
AntonotnaWang/3DCellSeg
Official implementation of "A novel deep learning-based 3D cell segmentation framework for future image-based disease detection". (However, I think the title should be "3DCellSeg - a robust deep learning-based 3D cell instance segmentation pipeline".)
ChristophReich1996/Yeast-in-Microstructures-Dataset
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
mberkay0/ConvNeXt-MaskRCNN
Train torchvision's MaskRCNN model using the ConvNeXt architecture as the backbone network.
delunapaolo/calipy
Real-time, interactive exploration of 3D image stacks
canfkoyuncu/IterativeHMinima
Iterative H-minima Based Marker-Controlled Watershed for Cell Nucleus Segmentation
simonguld/CellSegmentationTracker
A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy