Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis

Holly C. Gibbs; Holly C. Gibbs; Sakina M. Mota; Nathan A. Hart; Sun Won Min; Alex O. Vernino; Anna L. Pritchard; Anindito Sen; Stan Vitha; Sreeja Sarasamma; Avery L. McIntosh; Alvin T. Yeh; Arne C. Lekven; Dylan A. McCreedy; Dylan A. McCreedy; Kristen C. Maitland; Kristen C. Maitland; Lisa M. Perez

doi:10.3389/fcell.2021.739079

Frontiers in Cell and Developmental Biology (Nov 2021)

Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis

Holly C. Gibbs,
Holly C. Gibbs,
Sakina M. Mota,
Nathan A. Hart,
Sun Won Min,
Alex O. Vernino,
Anna L. Pritchard,
Anindito Sen,
Stan Vitha,
Sreeja Sarasamma,
Avery L. McIntosh,
Alvin T. Yeh,
Arne C. Lekven,
Dylan A. McCreedy,
Dylan A. McCreedy,
Kristen C. Maitland,
Kristen C. Maitland,
Lisa M. Perez

Affiliations

Holly C. Gibbs: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Holly C. Gibbs: Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
Sakina M. Mota: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Nathan A. Hart: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Sun Won Min: Department of Biology, Texas A&M University, College Station, TX, United States
Alex O. Vernino: Department of Biology, Texas A&M University, College Station, TX, United States
Anna L. Pritchard: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Anindito Sen: Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
Stan Vitha: Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
Sreeja Sarasamma: Department of Neurology, Baylor College of Medicine, Houston, TX, United States
Avery L. McIntosh: Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
Alvin T. Yeh: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Arne C. Lekven: Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
Dylan A. McCreedy: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Dylan A. McCreedy: Department of Biology, Texas A&M University, College Station, TX, United States
Kristen C. Maitland: Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
Kristen C. Maitland: Microscopy and Imaging Center, Texas A&M University, College Station, TX, United States
Lisa M. Perez: High Performance Research Computing, Texas A&M University, College Station, TX, United States

DOI: https://doi.org/10.3389/fcell.2021.739079
Journal volume & issue: Vol. 9

Abstract

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From the combined perspective of biologists, microscope instrumentation developers, imaging core facility scientists, and high performance computing experts, we discuss the challenges faced when selecting imaging and analysis tools in the field of light-sheet microscopy. Our goal is to provide a contextual framework of basic computing concepts that cell and developmental biologists can refer to when mapping the peculiarities of different light-sheet data to specific existing computing environments and image analysis pipelines. We provide our perspective on efficient processes for tool selection and review current hardware and software commonly used in light-sheet image analysis, as well as discuss what ideal tools for the future may look like.

Published in Frontiers in Cell and Developmental Biology

ISSN: 2296-634X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General)
Website: https://www.frontiersin.org/journals/cell-and-developmental-biology

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