Cell Segmentation

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

12 leaderboard tables shown for this task, 12 with rows (a “benchmark” on this site is a table with at least one row, as on /sota), ordered by row count. “Best model” is the first row in the archive's own order at snapshot; nothing is re-ranked here and metric direction is not recorded in the archive. PwC's Trend sparklines are not in the archive, so that column is omitted. 10 shown of 12 until expanded.

Syntology column: samples harvested from the paper's repositories and executed on synthesized fixtures; “ran” is not a correctness claim and does not order the table. A dash means no Syntology record for that paper, not a recorded non-run. Read from the graph 2026-09-24.

Libraries

Not in the archive: the export carries no per-task library table, so there is nothing to show at snapshot 2025-07-28.

Datasets archive 2025-07-28

22 datasets whose archive record lists this task, ordered by the archive's paper count.

Subtasks archive 2025-07-28

1 subtask in the archive's task tree.

Parent tasks archive 2025-07-28

Most implemented papers archive 2025-07-28

30 shown of 91 papers with code (178 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• U-Net: Convolutional Networks for Biomedical Image Segmentation
  18 May 2015 487 repositories listed Syntology ran 510 of 757 samples · 247 unverified · 426 pointer-only (licence)
  There is large consent that successful training of deep networks requires many thousand annotated training samples.
• SPPNet: A Single-Point Prompt Network for Nuclei Image Segmentation
  23 Aug 2023 6 repositories listed
  Compared to the segment anything model, SPPNet shows roughly 20 times faster inference, with 1/70 parameters and computational cost.
• Deep Learning in Single-Cell Analysis
  22 Oct 2022 6 repositories listed Syntology ran 1 of 4 samples · 3 unverified · 1 pointer-only (licence)
  Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages.
• DoubleU-Net: A Deep Convolutional Neural Network for Medical Image Segmentation
  8 Jun 2020 4 repositories listed Syntology ran 2 of 5 samples · 3 unverified · 5 pointer-only (licence)
  The encouraging results, produced on various medical image segmentation datasets, show that DoubleU-Net can be used as a strong baseline for both medical image segmentation and cross-dataset evaluation testing to…
• CellViT: Vision Transformers for Precise Cell Segmentation and Classification
  27 Jun 2023 3 repositories listed Syntology ran 1 of 1 samples · 0 unverified · 1 pointer-only (licence)
  Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications.
• Scribble2Label: Scribble-Supervised Cell Segmentation via Self-Generating Pseudo-Labels with Consistency
  23 Jun 2020 3 repositories listed
  Segmentation is a fundamental process in microscopic cell image analysis.
• Fully Unsupervised Diversity Denoising with Convolutional Variational Autoencoders
  10 Jun 2020 3 repositories listed
  Deep Learning based methods have emerged as the indisputable leaders for virtually all image restoration tasks.
• CE-Net: Context Encoder Network for 2D Medical Image Segmentation
  7 Mar 2019 3 repositories listed
  In this paper, we propose a context encoder network (referred to as CE-Net) to capture more high-level information and preserve spatial information for 2D medical image segmentation.
• Cell Detection with Star-convex Polygons
  9 Jun 2018 3 repositories listed Syntology ran 1 of 33 samples · 32 unverified · 2 pointer-only (licence)
  Automatic detection and segmentation of cells and nuclei in microscopy images is important for many biological applications.
• Microscopy Cell Segmentation via Convolutional LSTM Networks
  29 May 2018 3 repositories listed
  Live cell microscopy sequences exhibit complex spatial structures and complicated temporal behaviour, making their analysis a challenging task.
• Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing
  20 Apr 2023 2 repositories listed
  This strategy achieves self-learning by sharing knowledge between a principal model and a very light-weight collaborator model.
• MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy
  7 Dec 2022 2 repositories listed Syntology ran 4 of 11 samples · 7 unverified
  Cell segmentation is a fundamental task for computational biology analysis.
• Training a deep learning model for single-cell segmentation without manual annotation
  14 Dec 2021 2 repositories listed
  Generating training data is expensive and a major hindrance in the wider adoption of machine learning based methods for cell segmentation.
• Contour Proposal Networks for Biomedical Instance Segmentation
  7 Apr 2021 2 repositories listed
  We construct CPN models with different backbone networks, and apply them to instance segmentation of cells in datasets from different modalities.
• Instance Segmentation of Biomedical Images with an Object-aware Embedding Learned with Local Constraints
  21 Apr 2020 2 repositories listed
  The network is trained to output embedding vectors of similar directions for pixels from the same object, while adjacent objects are orthogonal in the embedding space, which effectively avoids the fusion of objects in a…
• Applying Faster R-CNN for Object Detection on Malaria Images
  25 Apr 2018 2 repositories listed
  Deep learning based models have had great success in object detection, but the state of the art models have not yet been widely applied to biological image data.
• Unsupervised cell segmentation by fast Gaussian Processes
  24 May 2025 1 repository listed
  Cell boundary information is crucial for analyzing cell behaviors from time-lapse microscopy videos.
• CellVTA: Enhancing Vision Foundation Models for Accurate Cell Segmentation and Classification
  1 Apr 2025 1 repository listed
  To address this problem, we propose CellVTA (Cell Vision Transformer with Adapter), a novel method that improves the performance of vision foundation models for cell instance segmentation by incorporating a CNN-based…
• Prompting Vision-Language Model for Nuclei Instance Segmentation and Classification
  27 Mar 2025 1 repository listed
  Nuclei instance segmentation and classification are a fundamental and challenging task in whole slide Imaging (WSI) analysis.
• COIN: Confidence Score-Guided Distillation for Annotation-Free Cell Segmentation
  14 Mar 2025 1 repository listed
  Cell instance segmentation (CIS) is crucial for identifying individual cell morphologies in histopathological images, providing valuable insights for biological and medical research.
• HistoSmith: Single-Stage Histology Image-Label Generation via Conditional Latent Diffusion for Enhanced Cell Segmentation and Classification
  12 Feb 2025 1 repository listed
  Experimental results demonstrate improvements in cell instance segmentation and classification, particularly for underrepresented cell types like neutrophils in the Conic dataset.
• CASC-AI: Consensus-aware Self-corrective AI Agents for Noise Cell Segmentation
  11 Feb 2025 1 repository listed
  The Consensus Matrix defines regions where both the AI and annotators agree on cell and non-cell annotations, which are prioritized with stronger supervision.
• Segmentation-free integration of nuclei morphology and spatial transcriptomics for retinal images
  8 Feb 2025 1 repository listed
  This study introduces SEFI (SEgmentation-Free Integration), a novel method for integrating morphological features of cell nuclei with spatial transcriptomics data.
• Mind the Gap: Evaluating Patch Embeddings from General-Purpose and Histopathology Foundation Models for Cell Segmentation and Classification
  4 Feb 2025 1 repository listed
  This study investigates the representation learning gap between these two categories by analyzing multi-level patch embeddings applied to cell instance segmentation and classification.
• Single cell resolution 3D imaging and segmentation within intact live tissues
  31 Jan 2025 1 repository listed
  Epithelial cells form diverse structures from squamous spherical organoids to densely packed pseudostratified tissues.
• CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models
  9 Jan 2025 1 repository listed
  Digital Pathology is a cornerstone in the diagnosis and treatment of diseases.
• CellSeg1: Robust Cell Segmentation with One Training Image
  2 Dec 2024 1 repository listed
  We introduce CellSeg1, a practical solution for segmenting cells of arbitrary morphology and modality with a few dozen cell annotations in 1 image.
• Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation
  18 Nov 2024 1 repository listed
  To overcome this, we propose a novel framework for synthesizing densely annotated 2D and 3D cell microscopy images using cascaded diffusion models.
• Cellpose+, a morphological analysis tool for feature extraction of stained cell images
  24 Oct 2024 1 repository listed
  Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics.
• Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-Based Cell Segmentation in Microscopy Images
  18 Oct 2024 1 repository listed
  To address these issues, we propose a novel framework called RA-SE-ASPP-Net, which incorporates Residual Blocks, Attention Mechanism, Squeeze-and-Excitation connection, and Atrous Spatial Pyramid Pooling to achieve…

Syntology lines on 6 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.