The paper introduces the Allen Cell and Structure Segmenter, an open-source toolkit for 3D segmentation of intracellular structures in fluorescence microscopy images, achieving high accuracy through classic and deep learning workflows.

bioRxiv · Dec 13, 2020 · PreprintCell Biology

Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable

M. P. Viana, J. Chen, T. A. Knijnenburg, R. Vasan, C. Yan, J. E. Arakaki, M. Bailey, B. Berry, A. Borensztejn, J. M. Brown, S. Carlson, J. A. Cass, B. Chaudhuri, K. R. Cordes Metzler, M. E. Coston, , Leung

The paper establishes quantitative rules for the locations, amounts, and variation of 25 cellular structures in human iPSCs using high-resolution imaging and analysis.

bioRxiv · Dec 8, 2020 · PreprintCell Biology

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

K. A. Gerbin, T. Grancharova, R. Donovan-Maiye, M. C. Hendershott, J. Brown, S. Q. Dinh, J. L. Gehring, M. Hirano, G. R. Johnson, A. Nath, A. Nelson, C. M. Roco, A. B. Rosenberg, M. F. Sluzewski, M. P. Viana, , R. N. Gunawardane

The paper integrates gene expression and sarcomere organization in hiPSC-derived cardiomyocytes to predict subcellular states and reveal correlations between transcript abundance and structural patterns.

bioRxiv · May 26, 2020Cell Biology

Scarless gene tagging of transcriptionally silent genes in hiPSCs to visualize cardiomyocyte sarcomeres in live cells

B. Roberts, J. Arakaki, K. A. Gerbin, H. Malik, A. Nelson, M. C. Hendershott, C. Hookway, S. A. Ludmann, I. A. Mueller, R. Yang, S. M. Rafelski, R. N. Gunawardane

The paper describes a CRISPR/Cas9 method to tag transcriptionally silent genes in hiPSCs with mEGFP, enabling visualization of sarcomeric proteins in live cardiomyocytes.

bioRxiv · Jun 9, 2018Cell Biology