cell-segmentation

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

deep-learning pytorch stitching segmentation datasets image-segmentation multiplex super-resolution immunohistochemical-images cell-segmentation digital-pathology pathology whole-slide-imaging cell-biology cloud-native-applications multitask-learning pathology-image pathology-gan immunohistochemistry ai-ready

UpdatedApr 28, 2025
Python

yaoguangluo /ETL_Unicorn

Star167

数据可视化, 数据挖掘, 数据处理 ETL分析

theme skin workflow data-mining etl workflow-engine data-visualization data-analysis applet batch-script component-architecture cell-segmentation nero pipline reused-component

UpdatedFeb 15, 2022
Java

Lee-Gihun /MEDIAR

Star151

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

pytorch biomedical multi-resolution cell-segmentation instance-segmentation cell-biology pytorch-implementation multi-modality pytorch-segmentation monai vision-transformer neurips-2022 miscroscopy

UpdatedApr 1, 2024
Python

FZJ-INM1-BDA /celldetection

Star136

Scalable Instance Segmentation using PyTorch & PyTorch Lightning.

deep-learning pytorch object-detection unet semantic-segmentation cell-segmentation cpn instance-segmentation mask-rcnn cell-detection fpn cell-counting celldetection

UpdatedApr 22, 2025
Python

amirhossein-kz /HiFormer

Star135

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)

transformers semantic-segmentation cell-segmentation multi-organ-segmentation medical-image-segmentation skin-lesion-segmentation segpc cell-segmenation

UpdatedMar 22, 2024
Jupyter Notebook

royerlab /ultrack

Star112

Cell tracking and segmentation software

gurobi cell-segmentation cell-tracking cell-tracking-challenge

UpdatedMay 1, 2025
Python

ChristophReich1996 /Cell-DETR

Star101

Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].

deep-learning synthetic-biology transformer attention cell-segmentation instance-segmentation system-biology bibm-2020 cell-detr

UpdatedMar 28, 2022
Python

okunator /cellseg_models.pytorch

Star91

Encoder-Decoder Cell and Nuclei segmentation models

ai ml pytorch microscopy cell-segmentation digital-pathology panoptic-segmentation nuclei-segmentation tissue-segmentation cellpose timm stardist hovernet omnipose

UpdatedApr 23, 2025
Python

mkang315 /ASF-YOLO

Star86

[IMAVIS] Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".

deep-neural-networks yolo medical-image-computing medical-image-processing cell-segmentation nucleus-detection computer-vision-algorithms instance-segmentation deep-learning-framework cell-detection medical-image-analysis data-science-bowl-2018 medical-image-segmentation nuclei-segmentation lesion-segmentation hematoxylin-eosin-staining breast-cancer-segmentation detection-segmentation-algorithm histopathology-image-analysis breast-cancer-cell

UpdatedMar 3, 2025
Python

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).

ai graphs segmentation cell-segmentation oncology single-cell-analysis graph-neural-networks spatial-transcriptomics spatial-omics xenium molecule-graphs