Author

Jakub Kaczmarzyk

Cold Spring Harbor LaboratoryORCID 0000-0002-5544-7577Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 2 Assay:imaging· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:dimensionality reduction· 1 Approach:experimental assay· 1

Frequent Co-Authors

Satrajit GhoshiD· 2 shared Aina PuceiD· 1 shared Akshaiy Narayanan· 1 shared Andy Botting· 1 shared Angela RentoniD· 1 shared Anibal Sólon HeinsfeldiD· 1 shared Anthony John HannaniD· 1 shared Ashley Wilton StewartiD· 1 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersNeuroscience

Satrajit GhoshORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Dissecting and directing pathology foundation models

Chanwoo Kim, Jakub Kaczmarzyk, Deepika Savant, Zhen Zhao, Peter K. Koo, Su‐In Lee

This paper introduces PICASSO, a framework that makes pathology foundation models interpretable and controllable by decomposing embeddings into human-interpretable visual concepts, enabling new biological insights and downstream applications.

bioRxiv · Jun 16, 2026 · PreprintPathology

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Angela Renton, Thuy Thanh Dao, Tom Johnstone, Oren Civier, Ryan P. Sullivan, David White, Paris Lyons, Benjamin Slade, David F. Abbott, Toluwani Joan Amos, Saskia Bollmann, Andy Botting, Megan E. J. Campbell, Jeryn Chang, Thomas Close, , Steffen Bollmann

Neurodesk provides a portable and reproducible neuroimaging analysis platform using software containers to enable accessible and flexible data analysis pipelines.

Nature Methods · Jan 8, 2024Peer-reviewedNeuroscience

LittleBrain: a gradient-based tool for the topographical interpretation of cerebellar neuroimaging findings

Xavier Guell, Mathias Goncalves, Jakub Kaczmarzyk, John D. E. Gabrieli, Jeremy Dan Schmahmann, Satrajit Ghosh

LittleBrain visualizes cerebellar neuroimaging data along newly identified functional gradients to enhance topographical interpretation.

PLoS ONE · Jan 16, 2019Peer-reviewedNeuroscience