Cell Segmentation

Cell Segmentation is a task of splitting a microscopic image domain into segments, which represent individual instances of cells. It is a fundamental step in many biomedical studies, and it is regarded as a cornerstone of image-based cellular research. Cellular morphology is an indicator of a physiological state of the cell, and a well-segmented image can capture biologically relevant morphological information.

Source: Cell Segmentation by Combining Marker-controlled Watershed and Deep Learning

Papers

Recently Added Most Hyped Most Active Needs Verification Most Verified

Showing 1–25 of 178 papers

Title	Date	Tasks	Status	Hype
Deep Learning in Single-Cell Analysis	Oct 22, 2022	Cell SegmentationDeep Learning	CodeCode Available	3
U-Net: Convolutional Networks for Biomedical Image Segmentation	May 18, 2015	Cell SegmentationCell Tracking	CodeCode Available	3
InstanSeg: an embedding-based instance segmentation algorithm optimized for accurate, efficient and portable cell segmentation	Aug 28, 2024	Cell SegmentationGPU	CodeCode Available	3
Cell Detection with Star-convex Polygons	Jun 9, 2018	Cell DetectionCell Segmentation	CodeCode Available	2
CellViT: Vision Transformers for Precise Cell Segmentation and Classification	Jun 27, 2023	Cell DetectionCell Segmentation	CodeCode Available	2
Omnipose: a high-precision, morphology-independent solution for bacterial cell segmentation	Nov 5, 2021	Cell SegmentationVocal Bursts Intensity Prediction	CodeCode Available	2
Exploiting Scale-Variant Attention for Segmenting Small Medical Objects	Jul 10, 2024	Cell SegmentationMRI segmentation	CodeCode Available	2
U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation	Jan 9, 2024	Cell SegmentationImage Segmentation	CodeCode Available	2
CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models	Jan 9, 2025	Cell SegmentationDataset Generation	CodeCode Available	2
LKCell: Efficient Cell Nuclei Instance Segmentation with Large Convolution Kernels	Jul 25, 2024	Cell SegmentationDecoder	CodeCode Available	1
Instance Segmentation of Biomedical Images with an Object-aware Embedding Learned with Local Constraints	Apr 21, 2020	Cell SegmentationInstance Segmentation	CodeCode Available	1
Local Label Point Correction for Edge Detection of Overlapping Cervical Cells	Oct 5, 2020	Cell SegmentationEdge Detection	CodeCode Available	1
Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps	Aug 8, 2023	Cell SegmentationCell Tracking	CodeCode Available	1
LIVECell—A large-scale dataset for label-free live cell segmentation	Aug 30, 2021	Cell SegmentationCultural Vocal Bursts Intensity Prediction	CodeCode Available	1
ICOS Protein Expression Segmentation: Can Transformer Networks Give Better Results?	Jun 23, 2022	Cell Segmentation	CodeCode Available	1
MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy	Dec 7, 2022	Cell SegmentationElectron Microscopy Image Segmentation	CodeCode Available	1
Exploring Unsupervised Cell Recognition with Prior Self-activation Maps	Aug 22, 2023	Cell DetectionCell Segmentation	CodeCode Available	1
An Instance Segmentation Dataset of Yeast Cells in Microstructures	Apr 15, 2023	Cell SegmentationImage Segmentation	CodeCode Available	1
Fully Unsupervised Diversity Denoising with Convolutional Variational Autoencoders	Jun 10, 2020	Cell SegmentationDenoising	CodeCode Available	1
Faster Mean-shift: GPU-accelerated clustering for cosine embedding-based cell segmentation and tracking	Jul 28, 2020	Cell SegmentationCell Tracking	CodeCode Available	1
Attention-Based Transformers for Instance Segmentation of Cells in Microstructures	Nov 19, 2020	Cell DetectionCell Segmentation	CodeCode Available	1
DoubleU-Net: A Deep Convolutional Neural Network for Medical Image Segmentation	Jun 8, 2020	Cell SegmentationColorectal Polyps Characterization	CodeCode Available	1
CellVTA: Enhancing Vision Foundation Models for Accurate Cell Segmentation and Classification	Apr 1, 2025	Cell SegmentationInstance Segmentation	CodeCode Available	1
HistoSmith: Single-Stage Histology Image-Label Generation via Conditional Latent Diffusion for Enhanced Cell Segmentation and Classification	Feb 12, 2025	Cell SegmentationImage Generation	CodeCode Available	1
Accurate and versatile 3D segmentation of plant tissues at cellular resolution	Jul 29, 2020	Cell Segmentationgraph partitioning	CodeCode Available	1

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All datasets Fluo-N2DL-HeLa LIVECell DIC-C2DH-HeLa EVICAN Fluo-N2DH-GOWT1 Fluo-N2DH-SIM+CoNSeP Fluo-C3DL-MDA231 MoNuSeg PanNuke PhC-C2DH-U373

Benchmark Results

#	Model	Metric	Claimed	Verified	Status
1	Dual U-Net (Neighbor distances)	SEG (~Mean IoU)	0.9	—	Unverified
2	DecLSTM	SEG (~Mean IoU)	0.84	—	Unverified
3	EncLSTM	SEG (~Mean IoU)	0.81	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Cascade Mask RCNN-ResNest-200	mask AP	47.9	—	Unverified
2	CenterMask-VoVNet2-FPN	mask AP	47.8	—	Unverified
3	Point2Mask	mask AP	43.53	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EncLSTM	SEG (~Mean IoU)	0.79	—	Unverified
2	DecLSTM	SEG (~Mean IoU)	0.51	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DeepCeNS	mask AP	52.56	—	Unverified
2	EVICAN-MRCNN	mask AP	32.2	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DecLSTM	SEG (~Mean IoU)	0.85	—	Unverified
2	EncLSTM	SEG (~Mean IoU)	0.85	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EncLSTM	SEG (~Mean IoU)	0.81	—	Unverified
2	DecLSTM	SEG (~Mean IoU)	0.8	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	PromptNu	Average Dice	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Dual U-Net (Neighbor distances)	SEG (~Mean IoU)	0.62	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	PromptNu	Average Dice	0.84	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	PromptNu	Average Dice	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EncLSTM	SEG (~Mean IoU)	0.84	—	Unverified