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

QuPath - Open-source bioimage analysis for research

StarDist - Object Detection with Star-convex Shapes

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

Segment Anything for Microscopy

Spatiotemporal modeling of spatial transcriptomics

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

数据可视化, 数据挖掘, 数据处理 ETL分析

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

Scalable Instance Segmentation using 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].

Cell tracking and segmentation software

Encoder-Decoder Cell and Nuclei segmentation models

[IMAVIS] 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

A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation

ClusterMap for multi-scale clustering analysis of spatial gene expression

StarDist plugin for napari