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References from COEXIST: Coordinated single-cell integration of serial multiplexed tissue images. Local targets link to admitted publications; unresolved targets remain external evidence.
Multiplex protein imaging in tumour biology
10.1038/s41568-023-00657-4 · 2024 · External reference
Best practices for technical reproducibility assessment of multiplex immunofluorescence
10.3389/fmolb.2021.660202 · 2021 · External reference
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes
2018 · External reference
Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer
10.1038/s41523-023-00605-3 · 2024 · External reference
A web-based software resource for interactive analysis of multiplex tissue imaging datasets
2022 · External reference
Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging
10.1038/s41596-019-0206-y · 2019 · External reference
Three-dimensional assessments are necessary to determine the true, spatially-resolved composition of tissues
2024 · External reference
Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer
2023 · External reference
The 3D revolution in cancer discovery
10.1158/2159-8290.cd-23-1499 · 2024 · External reference
Engineering the future of 3D pathology
2024 · External reference
Highly multiplexed 3D profiling of cell states and immune niches in human tumours
2025 · External reference
Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping
2024 · External reference
Simultaneous epitope and transcriptome measurement in single cells
10.1038/nmeth.4380 · 2017 · External reference
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
10.1186/s13073-017-0467-4 · 2017 · External reference
Methods and applications for single-cell and spatial multi-omics
10.1038/s41576-023-00580-2 · 2023 · External reference
High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers
10.1038/s43018-023-00576-1 · 2023 · External reference
Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis
10.1016/j.celrep.2017.03.037 · 2017 · External reference
Three-dimensional computer reconstructions from serial sections of cell nuclei
1988 · External reference
SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning
10.1038/s41598-020-74500-3 · 2020 · External reference
CODA: quantitative 3D reconstruction of large tissues at cellular resolution
10.1038/s41592-022-01650-9 · 2022 · External reference
3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding
10.3389/fbinf.2023.1275402 · 2023 · External reference
Virtual alignment of pathology image series for multi-gigapixel whole slide images
10.1038/s41467-023-40218-9 · 2023 · External reference
Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment
2022 · External reference
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq
10.1038/s41587-023-01676-0 · 2023 · External reference
Unresolved reference
External reference
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
10.1016/j.cell.2021.12.018 · 2022 · External reference
Spatially resolved multi-omics highlights cell-specific metabolic remodeling and interactions in gastric cancer
10.1038/s41467-023-38360-5 · 2023 · External reference
Computational methods for single-cell multi-omics integration and alignment
2022 · External reference
Comprehensive integration of single-cell data
10.1016/j.cell.2019.05.031 · 2019 · External reference
Joint variational autoencoders for multimodal imputation and embedding
10.1038/s42256-023-00663-z · 2023 · External reference
Bi-order multimodal integration of single-cell data
10.1186/s13059-022-02679-x · 2022 · External reference
10.1137/1.9781611972238
10.1137/1.9781611972238 · 2012 · External reference
Unresolved reference
External reference
Unsupervised topological alignment for single-cell multi-omics integration
2020 · External reference
Robust single-cell matching and multimodal analysis using shared and distinct features
10.1038/s41592-022-01709-7 · 2023 · External reference
Integration of spatial and single-cell data across modalities with weakly linked features
2023 · External reference
10.1109/cdc42340.2020.9304436
10.1109/cdc42340.2020.9304436 · External reference
Cellpose: a generalist algorithm for cellular segmentation
10.1038/s41592-020-01018-x · 2021 · External reference
Unresolved reference
External reference
On implementing 2D rectangular assignment algorithms
10.1109/taes.2016.140952 · 2016 · External reference
10.1109/iccv.2017.244
10.1109/iccv.2017.244 · External reference
Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms
10.1016/j.crmeth.2021.100053 · 2021 · External reference
On the dependency of cellular protein levels on mRNA abundance
10.1016/j.cell.2016.03.014 · 2016 · External reference
Highly multiplexed simultaneous detection of RNAs and proteins in single cells
10.1038/nmeth.3742 · 2016 · External reference
Immunohistochemistry and immunofluorescence
10.1007/978-1-0716-2780-8_26 · 2023 · External reference
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
10.1038/s41592-021-01308-y · 2022 · External reference
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
10.1038/s41587-021-01094-0 · 2022 · External reference
Deep learning based Nucleus Classification in pancreas histological images
2017 · External reference
scikit-image: image processing in Python
10.7717/peerj.453 · 2014 · External reference
Unresolved reference
External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
The spatial landscape of progression and immunoediting in primary melanoma at single-cell resolution
10.1158/2159-8290.cd-21-1357 · 2022 · External reference
Scikit-learn: machine learning in Python
2011 · External reference
Unresolved reference
2011 · External reference
Unresolved reference
External reference
The R project in statistical computing
10.11120/msor.2001.01010023 · 2001 · External reference
seaborn: statistical data visualization
10.21105/joss.03021 · 2021 · External reference
Matplotlib: a 2D graphics environment
10.1109/mcse.2007.55 · 2007 · External reference
Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web
10.1038/s41592-022-01482-7 · 2022 · External reference
10.31219/osf.io/y8thv
10.31219/osf.io/y8thv · External reference
