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References from Effects of segmentation errors on downstream-analysis in highly-multiplexed tissue imaging. Local targets link to admitted publications; unresolved targets remain external evidence.
High-dimensional in situ proteomics imaging to assess γδ T cells in spatial biology
10.1093/jleuko/qiad167 · 2024 · External reference
Organization of the human intestine at single-cell resolution
10.1038/s41586-023-05915-x · 2023 · External reference
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis
10.1093/bioinformatics/btad245 · 2023 · External reference
Deep profiling of mouse splenic architecture with CODEX multiplexed imaging
10.1016/j.cell.2018.07.010 · 2018 · External reference
Multiplexed ion beam imaging (MIBI) for characterization of the tumor microenvironment across tumor types
10.1038/s41374-020-0417-4 · 2020 · External reference
MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors
10.1038/s41598-022-05841-4 · 2022 · External reference
Imaging mass cytometry
10.1002/cyto.a.23053 · 2017 · External reference
A review on deep learning applications in highly multiplexed tissue imaging data analysis
10.3389/fbinf.2023.1159381 · 2023 · 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
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images
10.1186/s12859-022-04570-9 · 2022 · External reference
Cellpose 2.0: how to train your own model
10.1038/s41592-022-01663-4 · 2022 · External reference
10.1007/978-3-030-00934-2_30
10.1007/978-3-030-00934-2_30 · External reference
10.1109/wacv45572.2020.9093435
10.1109/wacv45572.2020.9093435 · External reference
10.1109/isbic56247.2022.9854534
10.1109/isbic56247.2022.9854534 · External reference
UnMICST: deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues
10.1038/s42003-022-04076-3 · 2022 · External reference
10.1109/isbi.2017.7950532
10.1109/isbi.2017.7950532 · External reference
Micro-Net: a unified model for segmentation of various objects in microscopy images
10.1016/j.media.2018.12.003 · 2019 · External reference
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
10.1038/s41592-019-0612-7 · 2019 · External reference
The multimodality cell segmentation challenge: toward universal solutions
10.1038/s41592-024-02233-6 · 2024 · External reference
Albumentations: fast and flexible image augmentations
10.3390/info11020125 · 2020 · External reference
Unresolved reference
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Unresolved reference
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Machine learning in python: main developments and technology trends in data science, machine learning, and artificial intelligence
10.3390/info11040193 · 2020 · External reference
Array programming with NumPy
10.1038/s41586-020-2649-2 · 2020 · External reference
10.1145/2833157.2833162
10.1145/2833157.2833162 · External reference
Unresolved reference
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The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense
10.1371/journal.pcbi.1012403 · 2024 · External reference
Large network community detection by fast label propagation
10.1038/s41598-023-29610-z · 2023 · External reference
Fast unfolding of communities in large networks
10.1088/1742-5468/2008/10/p10008 · 2008 · External reference
Unresolved reference
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Scikit-learn: machine learning in python
2011 · External reference
10.3115/981732.981751
10.3115/981732.981751 · External reference
Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin
2023 · External reference
Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data
10.1038/s41467-024-55214-w · 2025 · External reference
Spatial single-cell profiling and neighbourhood analysis reveal the determinants of immune architecture connected to checkpoint inhibitor therapy outcome in hepatocellular carcinoma
10.1136/gutjnl-2024-332837 · 2025 · External reference
A probabilistic u-net for segmentation of ambiguous images
2018 · External reference
10.1007/978-3-030-32245-8_14
10.1007/978-3-030-32245-8_14 · External reference
Stochastic segmentation networks: modelling spatially correlated aleatoric uncertainty
2020 · External reference
Nextflow enables reproducible computational workflows
10.1038/nbt.3820 · 2017 · External reference
Feature selection methods affect the performance of scRNA-sEq data integration and querying
10.1038/s41592-025-02624-3 · 2025 · External reference
