Author

Shenyi Li

California Institute of Technology

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Assay:spatial transcriptomics· 2 Approach:transformer / foundation model· 2 Organism:bacteria (other)· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Organism:human· 1 Assay:imaging· 1

Frequent Co-Authors

Caitlin Brown· 2 shared David Van ValeniD· 2 shared Elora Pradhan· 2 shared Martin AbtiD· 2 shared Rohit DilipiD· 2 shared Ross BarnowskiiD· 2 shared Yisong YueiD· 2 shared Ada Ates· 1 shared

Activity by Year

2023-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 43 mutual co-author links

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2 shared papersBioinformatics

Caitlin Brown

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Author profile →

2 papers

Recent·Most cited

Generalized cell phenotyping for spatial proteomics with language-informed vision models

Xuefei Wang, Rohit Dilip, Ahamed Raffey Iqbal, Yuval Bussi, Caitlin Brown, Elora Pradhan, Yashvardhan Jain, Kevin Yu, Shenyi Li, Martin Abt, Katy Börner, Leeat Keren, Yisong Yue, Ross Barnowski, David Van Valen

This paper introduces DeepCell Types, a language-informed vision model for spatial proteomics cell phenotyping that generalizes across diverse datasets and marker panels.

bioRxiv · Nov 2, 2024 · PreprintBioinformatics

CellSAM: A Foundation Model for Cell Segmentation

Uriah Israel, Markus Marks, Rohit Dilip, Qilin Li, Changhua Yu, Emily Laubscher, Ahamed Iqbal, Elora Pradhan, Ada Ates, Martin Abt, Caitlin Brown, Edward Pao, Shenyi Li, Alexander Pearson-Goulart, Pietro Perona, , David Van Valen

Bounding boxes from a transformer detector let the Segment Anything Model segment cells automatically; one generalist model beats generalist Cellpose and matches inter-annotator agreement across mammalian, yeast and bacterial images.

bioRxiv · Nov 17, 2023 · PreprintBioinformatics✦ In-depth digest