Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
Authors
Keywords
-
Journal
NATURE BIOTECHNOLOGY
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-11-19
DOI
10.1038/s41587-021-01094-0
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes
- (2021) Dylan Bannon et al. NATURE METHODS
- Democratising deep learning for microscopy with ZeroCostDL4Mic
- (2021) Lucas von Chamier et al. Nature Communications
- The single-cell pathology landscape of breast cancer
- (2020) Hartland W. Jackson et al. NATURE
- HSF1 phase transition mediates stress adaptation and cell fate decisions
- (2020) Giorgio Gaglia et al. NATURE CELL BIOLOGY
- The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
- (2020) Orit Rozenblatt-Rosen et al. CELL
- nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
- (2020) Reka Hollandi et al. Cell Systems
- Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front
- (2020) Christian M. Schürch et al. CELL
- DeepDistance: A multi-task deep regression model for cell detection in inverted microscopy images
- (2020) Can Fahrettin Koyuncu et al. MEDICAL IMAGE ANALYSIS
- Accurate and versatile 3D segmentation of plant tissues at cellular resolution
- (2020) Adrian Wolny et al. eLife
- Array programming with NumPy
- (2020) Charles R. Harris et al. NATURE
- NuSeT: A deep learning tool for reliably separating and analyzing crowded cells
- (2020) Linfeng Yang et al. PLoS Computational Biology
- Cellpose: a generalist algorithm for cellular segmentation
- (2020) Carsen Stringer et al. NATURE METHODS
- Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
- (2019) Chee-Huat Linus Eng et al. NATURE
- ilastik: interactive machine learning for (bio)image analysis
- (2019) Stuart Berg et al. NATURE METHODS
- Stable FIX Expression and Durable Reductions in Bleeding and Factor IX Consumption for up to 4 Years Following AMT-060 Gene Therapy in Adults with Severe or Moderate-Severe Hemophilia B
- (2019) Wolfgang Miesbach et al. BLOOD
- ImJoy: an open-source computational platform for the deep learning era
- (2019) Wei Ouyang et al. NATURE METHODS
- Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
- (2019) Juan C. Caicedo et al. NATURE METHODS
- MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure
- (2019) Leeat Keren et al. Science Advances
- Hover-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images
- (2019) Simon Graham et al. MEDICAL IMAGE ANALYSIS
- A Multi-Organ Nucleus Segmentation Challenge
- (2019) Neeraj Kumar et al. IEEE TRANSACTIONS ON MEDICAL IMAGING
- Quanti.us: a tool for rapid, flexible, crowd-based annotation of images
- (2018) Alex J. Hughes et al. NATURE METHODS
- Three-dimensional intact-tissue sequencing of single-cell transcriptional states
- (2018) Xiao Wang et al. SCIENCE
- CellProfiler 3.0: Next-generation image processing for biology
- (2018) Claire McQuin et al. PLOS BIOLOGY
- Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes
- (2018) Jia-Ren Lin et al. eLife
- Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry
- (2018) Daniel Schulz et al. Cell Systems
- Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging
- (2018) Yury Goltsev et al. CELL
- A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging
- (2018) Leeat Keren et al. CELL
- Object-Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images
- (2018) Can Fahrettin Koyuncu et al. CYTOMETRY PART A
- CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation
- (2018) Matthias G. Haberl et al. NATURE METHODS
- Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region
- (2018) Jeffrey R. Moffitt et al. SCIENCE
- Defective decidualization during and after severe preeclampsia reveals a possible maternal contribution to the etiology
- (2017) Tamara Garrido-Gomez et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- QuPath: Open source software for digital pathology image analysis
- (2017) Peter Bankhead et al. Scientific Reports
- Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets
- (2016) Ilya Belevich et al. PLOS BIOLOGY
- Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
- (2016) David A. Van Valen et al. PLoS Computational Biology
- Spatially resolved, highly multiplexed RNA profiling in single cells
- (2015) K. H. Chen et al. SCIENCE
- Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
- (2014) Charlotte Giesen et al. NATURE METHODS
- Single-cell in situ RNA profiling by sequential hybridization
- (2014) Eric Lubeck et al. NATURE METHODS
- Highly Multiplexed Subcellular RNA Sequencing in Situ
- (2014) J. H. Lee et al. SCIENCE
- scikit-image: image processing in Python
- (2014) Stéfan van der Walt et al. PeerJ
- Immunology of the Maternal-Fetal Interface
- (2013) Adrian Erlebacher Annual Review of Immunology
- Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Update
- (2013) Antonio C. Wolff et al. JOURNAL OF CLINICAL ONCOLOGY
- Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue
- (2013) M. J. Gerdes et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A colorful future of quantitative pathology: validation of Vectra technology using chromogenic multiplexed immunohistochemistry and prostate tissue microarrays
- (2012) Wei Huang et al. HUMAN PATHOLOGY
- Annotated high-throughput microscopy image sets for validation
- (2012) Vebjorn Ljosa et al. NATURE METHODS
- Icy: an open bioimage informatics platform for extended reproducible research
- (2012) Fabrice de Chaumont et al. NATURE METHODS
- Fiji: an open-source platform for biological-image analysis
- (2012) Johannes Schindelin et al. NATURE METHODS
- NIH Image to ImageJ: 25 years of image analysis
- (2012) Caroline A Schneider et al. NATURE METHODS
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started