There are 20 repositories under cell-segmentation topic.
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Segment Anything for Microscopy
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
数据可视化, 数据挖掘, 数据处理 ETL分析
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
Spatiotemporal modeling of spatial transcriptomics
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
Instance Segmentation with PyTorch & PyTorch Lightning.
HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)
Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].
Encoder-Decoder Cell and Nuclei segmentation models
Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".
PyTorch implementation of several neural network models for cellular image segmentation
ClusterMap for multi-scale clustering analysis of spatial gene expression
For cell segmentation and tracking.
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
StarDist plugin for napari
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation
Automated identification of cell boundaries from the pathological video data
Tissue Cancer Segmentation project using multiple segmentation networks
A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
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".)
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
Real-time, interactive exploration of 3D image stacks
Iterative H-minima Based Marker-Controlled Watershed for Cell Nucleus Segmentation
A style-aware deep learning model for adaptive cell instance segmentation by contrastive fine-tuning.
Train torchvision's MaskRCNN model using the ConvNeXt architecture as the backbone network.
(Biological) Cell Proposal Network for Microscopy Image Analysis
A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy