Results

PaperS7526

Graph Fourier transform for spatial omics representation and analyses of complex organs

Yuzhou Chang, Jixin Liu, Yi Jiang, Anjun Ma, Yao Yu Yeo, Qi Guo, Megan McNutt, Jordan E Krull, Scott J Rodig, Dan H Barouch, Garry P Nolan, Dong Xu, Sizun Jiang, Zihai Li, Bingqiang Liu, Qin Ma. ebi.ac.uk. August 29, 2024.

SpaGFT represents spatial data using graph topology and low-frequency assumptions. Benchmarks vary by dataset, and some methods perform better in particular examples. Selected marker references, repeated tissue regions and alternate analysis methods do not independently establish biological causation or patient replication.

Main text and selected supporting materials read
PaperS7555

CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images

Michael Y. Lee, Jacob S. Bedia, Salil S. Bhate, Graham L. Barlow, Darci Phillips, Wendy J. Fantl, Garry P. Nolan, Christian M. Schürch. ebi.ac.uk. January 18, 2022.

CellSeg combines a pretrained nucleus-segmentation model with image scaling, stitching, mask expansion and pixel statistics. Historical benchmark scores and representative tissue examples have different provenance and settings; densely packed tissue remains difficult. A colorectal comparison reuses 140 samples from 35 people and provides author-described gating and correlation. Correlation does not establish exhaustive cell truth or universal clinical accuracy. Source-native metric definitions, count conflicts and caption errors are preserved.

Supplied text and six figures read
PaperS7599

Complex Mammalian-like Hematopoietic System Found in a Colonial Chordate

Benyamin Rosental, Mark Kowarsky, Jun Seita, Daniel M. Corey, Katherine J. Ishizuka, Karla J. Palmeri, Shih-Yu Chen, Rahul Sinha, Jennifer Okamoto, Gary Mantalas, Lucia Manni, Tal Raveh, D. Nathaniel Clarke, Jonathan M. Tsai, Aaron M. Newman, Norma F. Neff, Garry P. Nolan, Stephen R. Quake, Irving L. Weissman, Ayelet Voskoboynik. ebi.ac.uk. December 5, 2018.

The authors report candidate blood-forming and immune-cell populations in a colonial tunicate, using expression comparisons, transplantation and functional assays. Mammalian similarities remain qualified by missing lymphoid signatures, cross-reactivity, autofluorescence and incomplete stem-cell benchmarks.

Complete supplied manuscript and tables; apparatus missing

A curated public selection. Source review describes what was read; it does not establish that a claim is true. Our research approach