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Cell Segmentation

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하위 태스크: 1
평가표: 12
보존된 평가 기록: 20

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

코드

관련 논문과 평가 결과에 연결된 구현입니다. 출처에서 확인된 저자 구현에는 공식 코드 표시가 있습니다.

https://github.com/itmo-mmrm-lab/cellpose

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Cellpose+, a morphological analysis tool for feature extraction of stained cell images

https://github.com/jiyuuchc/lacss

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Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing

https://github.com/jiyuuchc/lacss_jax

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Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing

https://github.com/kuku-sichuan/ComparisonDetector

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Comparison-Based Convolutional Neural Networks for Cervical Cell/Clumps Detection in the Limited Data Scenario

https://github.com/lee-gihun/mediar

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MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy

https://github.com/lhaof/cellseg

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Multi-stream Cell Segmentation with Low-level Cues for Multi-modality Images

https://github.com/looooongChen/instance_segmentation_with_pixel_embeddings

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Instance Segmentation of Biomedical Images with an Object-aware Embedding Learned with Local Constraints

https://github.com/masqm/Faster-Mean-Shift

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Faster Mean-shift: GPU-accelerated clustering for cosine embedding-based cell segmentation and tracking

https://github.com/nachifur/LLPC

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Local Label Point Correction for Edge Detection of Overlapping Cervical Cells

https://github.com/naivete5656/WSISPDR

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Weakly Supervised Cell Instance Segmentation by Propagating from Detection Response

https://github.com/omfsdigital/cyto-r-cnn

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Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images

https://github.com/omicsml/dance

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Deep Learning in Single-Cell Analysis

https://github.com/ounissimehdi/phagostat

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PhagoStat a scalable and interpretable end to end framework for efficient quantification of cell phagocytosis in neurodegenerative disease studies

https://github.com/ozguncck/recovering-the-imperfect

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Recovering the Imperfect: Cell Segmentation in the Presence of Dynamically Localized Proteins

https://github.com/ranchogoose/morphoseg

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MorphoSeg: An Uncertainty-Aware Deep Learning Method for Biomedical Segmentation of Complex Cellular Morphologies

https://github.com/rb-sl/expertdrivennuclei

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An expert-driven data generation pipeline for histological images

https://github.com/rongzhou7/ttt-unet

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TTT-Unet: Enhancing U-Net with Test-Time Training Layers for Biomedical Image Segmentation

https://github.com/roydenwa/efficient-cell-seg

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EfficientCellSeg: Efficient Volumetric Cell Segmentation Using Context Aware Pseudocoloring

https://github.com/royerlab/ultrack

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Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps

https://github.com/ruveydayilmaz0/bvdm

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Annotated Biomedical Video Generation using Denoising Diffusion Probabilistic Models and Flow Fields

https://github.com/ruveydayilmaz0/cascaded_diffusion

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Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation

https://github.com/scverse/scvi-tools

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Deep Learning in Single-Cell Analysis

https://github.com/shjo-april/coin

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COIN: Confidence Score-Guided Distillation for Annotation-Free Cell Segmentation

https://github.com/stardist/stardist

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Cell Detection with Star-convex Polygons

https://github.com/stegmaierj/CellShapeAnalysis

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Semi-Automatic Generation of Tight Binary Masks and Non-Convex Isosurfaces for Quantitative Analysis of 3D Biological Samples

https://github.com/stegmaierj/Cellpose3D

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Robust 3D Cell Segmentation: Extending the View of Cellpose

https://github.com/tio-ikim/cellvit

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CellViT: Vision Transformers for Precise Cell Segmentation and Classification

https://github.com/tio-ikim/cellvit-plus-plus

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CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models

https://github.com/tushaarkataria/histopathology-domain-specific-pretraining

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To pretrain or not to pretrain? A case study of domain-specific pretraining for semantic segmentation in histopathology

https://github.com/uhlmanngroup/AURA-Net

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aura-net : robust segmentation of phase-contrast microscopy images with few annotations

https://github.com/uncertaintyquantification/cell_segmentation

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Unsupervised cell segmentation by fast Gaussian Processes

https://github.com/vanvalenlab/deepcell-tf

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Deep Learning in Single-Cell Analysis

https://github.com/wukevin/babel

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Deep Learning in Single-Cell Analysis

https://github.com/xieenze/PolarMask

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PolarMask++: Enhanced Polar Representation for Single-Shot Instance Segmentation and Beyond

https://github.com/xq141839/sppnet

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SPPNet: A Single-Point Prompt Network for Nuclei Image Segmentation

https://github.com/yijingru/KG_Instance_Segmentation

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Multi-scale Cell Instance Segmentation with Keypoint Graph based Bounding Boxes

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