5 papers for “Cell annotation”

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PaperS7678

Annotation-free discovery of disease-relevant cells in single-cell datasets

Erin Craig, Timothy J Keyes, Jolanda Sarno, Jeremy P D’Silva, Pablo Domizi, Maxim Zaslavsky, Albert Tsai, David Glass, Garry P Nolan, Trevor Hastie, Robert Tibshirani, Kara L Davis. ebi.ac.uk. August 27, 2025.

This Nolan-coauthored computational study estimates disease-associated cells using patient disease labels and a healthy baseline, without requiring expert cell annotations. Reported leukemia examples support a research method, with stronger expert-label benchmarks, small patient cohorts and assumptions that limit interpretation. Millions of measured cells do not imply millions of independent patients. Disclosed NIH support does not establish a classified programme or UAP access.

Complete supplied XML text; graphics, algorithms and supplements unreviewed

PaperS7570

MAPS: pathologist-level cell type annotation from tissue images through machine learning

Muhammad Shaban, Yunhao Bai, Huaying Qiu, Shulin Mao, Jason Yeung, Yao Yu Yeo, Vignesh Shanmugam, Han Chen, Bokai Zhu, Jason L Weirather, Garry P Nolan, Margaret A Shipp, Scott J Rodig, Sizun Jiang, Faisal Mahmood. ebi.ac.uk. January 2, 2024.

MAPS uses expert-labelled protein-expression data to classify cells. The authors report strong results within datasets, while acknowledging leakage risk from splitting one patient’s CODEX image by cells. Performance falls across cohorts and competing methods sometimes do better. Nolan is a coauthor and supervisor; disclosed commercial interests, reporting differences and missing original materials accompany the findings.

Complete supplied article and supplement text read; original and tiny-label gaps

PaperS7553

Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data

John W. Hickey, Yuqi Tan, Garry P. Nolan, Yury Goltsev. ebi.ac.uk. August 13, 2021.

The study compares 20 cell-annotation pipelines using four healthy-colon tissue blocks from one donor. Agreement improves with broader labels, but both reference sets use the same images and one explicitly favors a pipeline being evaluated. The authors recommend checking expression patterns and image locations when assigning cell types. Marker counts, a worked F-score example and several caption or settings inconsistencies remain documented. These results do not establish universal clinical accuracy or a UAP connection.

Supplied text and scoped apparatus read

PaperS7568

SPACEc: a streamlined, interactive Python workflow for multiplexed image processing and analysis

Yuqi Tan, Tim N Kempchen, Martin Becker, Maximilian Haist, Dorien Feyaerts, Jiaqi Liu, Marieta Toma, Yang Xiao, Graham Su, Andrew J Rech, Michael Hölzel, Rong Fan, John W Hickey, Garry P Nolan. ebi.ac.uk. November 27, 2025.

SPACEc combines spatial proteomics processing, cell annotation and neighbourhood analysis. Nolan is credited with supervision. The supplied article, static supplement and reporting form were reviewed; peer-review correspondence is partly read. Reused tissues, expert labels and nested cell counts limit independent replication. Computational comparisons depend on dataset, platform, normalization and metric definitions; funding does not establish a UAP programme.

Complete supplied main and static supplement text read; peer review partial

PaperS7560

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

Julia Kennedy‐Darling, Salil S Bhate, John W Hickey, Sarah Black, Graham L Barlow, Gustavo Vazquez, Vishal G Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M Schürch, Garry P Nolan. ebi.ac.uk. March 10, 2021.

The authors demonstrate repeated three-color imaging of DNA-tagged antibodies on five human tissue sections from five donors. Millions of segmented cells do not become independent human subjects. Barcode and repeated-cycle validation experiments each have one experimental replicate. Cell-type assignment and spatial associations depend on segmentation, markers and manual annotation. Barcode counts, omitted sequences, reagent labels, geometry and timing remain inconsistent in the supplied material. Nolan is a cosenior and corresponding coauthor.

Complete supplied text and received apparatus read