cell-segmentation

There are 22 repositories under cell-segmentation topic.

cellpose
MouseLand / cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
cell-biology cell-segmentation segmentation
Language:Python 1945
qupath / qupath
QuPath - Open-source bioimage analysis for research
bioimage-informatics image-processing digital-pathology pathology machine-learning cell-segmentation whole-slide-imaging bioimage-analysis cell-analysis imagej opencv groovy histology javafx tissue-microarray-analysis computational-pathology
Language:Java 1238
stardist
stardist / stardist
StarDist - Object Detection with Star-convex Shapes
bioimage-analysis cell-segmentation nuclei-segmentation object-detection deep-learning python
Language:Python 1120
computational-cell-analytics / micro-sam
Segment Anything for Microscopy
microscopy-images segment-anything segmentation cell-segmentation napari nuclei-segmentation mitochondria-segmentation micro-sam bioimage-analysis
Language:Jupyter Notebook 608
TissueImageAnalytics / tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
python computational-pathology whole-slide-imaging deep-learning digital-pathology histopathology image-analysis machine-learning tissue-analysis tissue-segmentation cell-classification cell-segmentation medical-image-analysis stain-normalization
Language:Python 482
aristoteleo / spateo-release
Spatiotemporal modeling of spatial transcriptomics
3d-reconstruction cell-segmentation spatial-transcriptomics spatiotemporal
Language:Python 318
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]
multiplex immunohistochemical-images immunohistochemistry deep-learning multitask-learning pathology pathology-image pathology-gan segmentation cell-segmentation cell-biology cloud-native-applications pytorch ai-ready datasets image-segmentation digital-pathology stitching super-resolution whole-slide-imaging
Language:Python 221
oist / Usiigaci
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
tensorflow python3 keras resnet-101 visualization cell-biology cell-segmentation machine-learning tracking trackpy mask-rcnn matplotlib
Language:Jupyter Notebook 197
yaoguangluo / ETL_Unicorn
数据可视化, 数据挖掘, 数据处理 ETL分析
etl data-mining data-visualization pipline reused-component applet data-analysis component-architecture batch-script theme skin nero cell-segmentation workflow-engine workflow
Language:Java 170
royerlab / ultrack
Cell tracking and segmentation software
cell-segmentation cell-tracking cell-tracking-challenge gurobi
Language:Python 155
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"
biomedical cell-biology cell-segmentation instance-segmentation monai multi-modality neurips-2022 pytorch pytorch-implementation pytorch-segmentation vision-transformer miscroscopy multi-resolution
Language:Python 153
FZJ-INM1-BDA / celldetection
Scalable Instance Segmentation using PyTorch & PyTorch Lightning.
cell-detection celldetection pytorch deep-learning instance-segmentation cell-segmentation cell-counting semantic-segmentation unet mask-rcnn fpn cpn object-detection
Language:Python 145
amirhossein-kz / HiFormer
HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)
cell-segmenation cell-segmentation medical-image-segmentation multi-organ-segmentation segpc semantic-segmentation skin-lesion-segmentation transformers
Language:Jupyter Notebook 140
Cell-DETR
ChristophReich1996 / Cell-DETR
Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].
bibm-2020 deep-learning attention instance-segmentation cell-segmentation synthetic-biology cell-detr transformer system-biology
Language:Python 107
mkang315 / ASF-YOLO
[IMAVIS] Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".
breast-cancer-segmentation cell-detection cell-segmentation computer-vision-algorithms data-science-bowl-2018 deep-learning-framework deep-neural-networks detection-segmentation-algorithm hematoxylin-eosin-staining histopathology-image-analysis instance-segmentation lesion-segmentation medical-image-analysis medical-image-computing medical-image-processing medical-image-segmentation nuclei-segmentation nucleus-detection yolo breast-cancer-cell
Language:Python 101
okunator / cellseg_models.pytorch
Encoder-Decoder Cell and Nuclei segmentation models
ai cell-segmentation cellpose digital-pathology hovernet microscopy ml nuclei-segmentation omnipose panoptic-segmentation pytorch stardist timm tissue-segmentation
Language:Python 95
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).
ai cell-segmentation graph-neural-networks graphs oncology segmentation single-cell-analysis spatial-omics spatial-transcriptomics xenium molecule-graphs
Language:HTML 79
Omid-Nejati / BEFUnet
A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation
cell-segmentation colab-notebook deep-learning hybrid-transformer multi-organ-segmentation segmentation skin-lesion-segmentation transformers medical medical-imaging
Language:Python 61
marshuang80 / cell-segmentation
PyTorch implementation of several neural network models for cellular image segmentation
segmentation cell-segmentation pytorch unet
Language:Jupyter Notebook 48
wanglab-broad / ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
in-situ-sequencing spatial-transcriptomics single-cell-analysis spatial-omics bioinformatics cell-segmentation transcriptomics
Language:Jupyter Notebook 46
nadeemlab / ImPartial
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
cell-biology cell-segmentation deep-learning denoising instance-segmentation interactive pytorch segmentation
Language:Jupyter Notebook 40
stardist / stardist-napari
StarDist plugin for napari
cell-segmentation deep-learning nuclei-segmentation object-detection napari napari-plugin
Language:Python 39
ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
cell-segmentation single-cell-analysis imaging-mass-cytometry immunofluorescence histological-images gating tissue-analysis tissue-classification histology bioimage-analysis bioimaging bioimage-tools bioimage-informatics mcd imc life-sciences-image ome-tiff image-analysis-workflows
Language:R 38
SAIL-GuoLab / Cell_Segmentation_and_Tracking
For cell segmentation and tracking.
deep-learning cell-segmentation residual-attention-network u-net cell-tracking
Language:Jupyter Notebook 36
Kartezio
KevinCortacero / Kartezio
Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming
computer-vision few-shot-learning frugal-ai image-processing local-ai cartesian-genetic-programming sustainable-ai transparent-ai cell-segmentation instance-segmentation semantic-segmentation
Language:Python 35
SlavkoPrytula / IAUNet
[CVPRW 2025] Official code of "IAUNet: Instance-Aware U-Net"
biomedical-imaging brightfield cell-segmentation computer-vision dataset instance-segmentation microscopy query-based semantic-segmentation transformers unet
Language:Python 29
iitmcvg / Cell-Segmentation
Automated identification of cell boundaries from the pathological video data
structured-forests cell-segmentation computer-vision
Language:Python 24
ariel-waisman / LabelsToROIs
A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
label-images imagej fiji-plugin fiji computer-vision segmentation image-analysis cell-segmentation
Language:Python 23
HistoJS
Mmasoud1 / HistoJS
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
cell-cell-interaction cell-segmentation mibiscope multiplexed-imaging multiplexed-imaging-analysis ome-tiff phenotyping proteomics proteomics-data-analysis single-cell whole-slide-imaging digital-slide-archive image-processing multichannel spatial-biology spatial-data-analysis
Language:JavaScript 23
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".)
cell-segmentation deep-learning
Language:Jupyter Notebook 22
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.
3d-segmentation cell-biology cell-segmentation image-analysis python
Language:MATLAB 22
kdha0727 / cancer-instance-segmentation-from-tissue
Tissue Cancer Segmentation project using multiple segmentation networks
cancer-detection cell-segmentation medical-imaging pytorch segmentation tissue-segmentation
Language:Python 22
simonguld / CellSegmentationTracker
A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy
active-matter bioinformatics-pipeline biophysics biostatistics cell-segmentation cell-tracking
Language:Jupyter Notebook 16
ChristophReich1996 / Yeast-in-Microstructures-Dataset
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
cell-segmentation dataset deep-learning embc evaluation evaluation-framework evaluation-metrics instance-segmentation medical-imaging panoptic-segmentation segmentation yeast-dataset
Language:Python 14
mberkay0 / ConvNeXt-MaskRCNN
Train torchvision's MaskRCNN model using the ConvNeXt architecture as the backbone network.
cellsegmentation convnext maskrcnn pytorch torchvision celltrackingchallenge image-segmentation cell-motility cell-segmentation deep-learning
Language:Python 14
delunapaolo / calipy
Real-time, interactive exploration of 3D image stacks
calcium-imaging gui python numpy pyqtgraph pyqt microscopy live-microscopy exploratory-data-analysis exploratory-data-visualizations interactive-analysis segmentation cell-segmentation fluorescence-microscopy-imaging fluorescence-data fluorescence-traces
Language:Python 13

cell-segmentation

MouseLand / cellpose

qupath / qupath

stardist / stardist

computational-cell-analytics / micro-sam

TissueImageAnalytics / tiatoolbox

aristoteleo / spateo-release

nadeemlab / DeepLIIF

oist / Usiigaci

yaoguangluo / ETL_Unicorn

royerlab / ultrack

Lee-Gihun / MEDIAR

FZJ-INM1-BDA / celldetection

amirhossein-kz / HiFormer

ChristophReich1996 / Cell-DETR

mkang315 / ASF-YOLO

okunator / cellseg_models.pytorch

EliHei2 / segger_dev

Omid-Nejati / BEFUnet

marshuang80 / cell-segmentation

wanglab-broad / ClusterMap

nadeemlab / ImPartial

stardist / stardist-napari

ciccalab / SIMPLI

SAIL-GuoLab / Cell_Segmentation_and_Tracking

KevinCortacero / Kartezio

SlavkoPrytula / IAUNet

iitmcvg / Cell-Segmentation

ariel-waisman / LabelsToROIs

Mmasoud1 / HistoJS

AntonotnaWang / 3DCellSeg

DanuserLab / u-segment3D

kdha0727 / cancer-instance-segmentation-from-tissue

simonguld / CellSegmentationTracker

ChristophReich1996 / Yeast-in-Microstructures-Dataset

mberkay0 / ConvNeXt-MaskRCNN

delunapaolo / calipy