Rafelski, Susanne M.

Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

Roberts, B., Haupt, A., Tucker, A., Grancharova, T., Arakaki, J., Fuqua, M. A., Nelson, A., Hookway, C., Ludmann, S. A., Mueller, I. A., et al. (2017) · Molecular Biology of the Cell

CRISPR and Genetic EngineeringPluripotent Stem Cells Research

Cited by 262

Understanding metric-related pitfalls in image analysis validation

Reinke, A., Tizabi, M. D., Baumgartner, M., Eisenmann, M., Heckmann-Nötzel, D., Kavur, A. E., Rädsch, T., Sudre, C. H., Acion, L., Antonelli, M., et al. (2024) · Nature Methods

Cell Image Analysis TechniquesMedical Image Segmentation Techniques

Cited by 241

Integrated intracellular organization and its variations in human iPS cells

Viana, M. P., Chen, J., Knijnenburg, T. A., Vasan, R., Yan, C., Arakaki, J. E., Bailey, M., Berry, B., Borensztejn, A., Brown, E. M., et al. (2023) · Nature

Cell Image Analysis TechniquesPluripotent Stem Cells Research

Cited by 132

The Allen Cell and Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images

Chen, J., Ding, L., Viana, M. P., Lee, H., Sluezwski, M. F., Morris, B., Hendershott, M. C., Yang, R., Mueller, I. A., & Rafelski, S. M. (2018) · bioRxiv (Cold Spring Harbor Laboratory)

Cell Image Analysis TechniquesMedical Image Segmentation Techniques

Cited by 99

Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Gerbin, K. A., Grancharova, T., Donovan-Maiye, R., Hendershott, M. C., Brown, J., Dinh, S. Q., Gehring, J. L., Hirano, M., Johnson, G. R., Nath, A., et al. (2020) · Cell Systems

Single-cell and spatial transcriptomicsPluripotent Stem Cells Research

Cited by 59

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Gerbin, K. A., Grancharova, T., Donovan-Maiye, R. M., Hendershott, M. C., Anderson, H. G., Brown, J. M., Chen, J., Dinh, S. Q., Gehring, J. L., Johnson, G. R., et al. (2021) · Cell Systems

Single-cell and spatial transcriptomicsPluripotent Stem Cells Research

Cited by 59

Interpretable representation learning for 3D multi-piece intracellular structures using point clouds

Vasan, R., Ferrante, A. J., Borensztejn, A., Frick, C. L., Garrison, P., Gaudreault, N., Mogre, S. S., Mohammed, F. S., Morris, B., Pires, G. G., et al. (2025) · Nature Methods

Cell Image Analysis TechniquesTopological and Geometric Data Analysis

Cited by 7

Automated hiPSC culture and sample preparation for 3D live cell microscopy

Coston, M. E., Gregor, B. W., Arakaki, J., Borensztejn, A., Do, T. P., Fuqua, M. A., Haupt, A., Hendershott, M. C., Leung, W., Mueller, I. A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory)

Cell Image Analysis TechniquesPluripotent Stem Cells Research

Cited by 6

Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories

Dixon, J. C., Frick, C. L., Leveille, C. L., Garrison, P., Lee, P. A., Mogre, S. S., Morris, B., Nivedita, N., Vasan, R., Chen, J., et al. (2024) · Cell Systems

Cell Image Analysis TechniquesGene Regulatory Network Analysis

Cited by 3

Cell shapes decode molecular phenotypes in image-based spatial proteomics

Le, T., Leineweber, W. D., Viana, M. P., Cesnik, A., Hansen, J. N., Ouyang, W., Rafelski, S. M., & Lundberg, E. (2026) · Cell Systems

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

Cited by 3

Cell shapes decode molecular phenotypes in image-based spatial proteomics

Le, T., Leineweber, W. D., Viana, M. P., Cesnik, A., Hansen, J. N., Ouyang, W., Rafelski, S. M., & Lundberg, E. (2025) · Cell Systems

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

Cited by 3