Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis
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 con...
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Frontiers Media S.A.
2021
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oai:doaj.org-article:7b9c40c88b904acc819188e096001d6f2021-11-10T17:30:33ZNavigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis2296-634X10.3389/fcell.2021.739079https://doaj.org/article/7b9c40c88b904acc819188e096001d6f2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fcell.2021.739079/fullhttps://doaj.org/toc/2296-634XFrom 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.Holly C. GibbsHolly C. GibbsSakina M. MotaNathan A. HartSun Won MinAlex O. VerninoAnna L. PritchardAnindito SenStan VithaSreeja SarasammaAvery L. McIntoshAlvin T. YehArne C. LekvenDylan A. McCreedyDylan A. McCreedyKristen C. MaitlandKristen C. MaitlandLisa M. PerezFrontiers Media S.A.articlelight-sheetimage analysisparallel processingmultiview deconvolutiontool selectionBiology (General)QH301-705.5ENFrontiers in Cell and Developmental Biology, Vol 9 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
light-sheet image analysis parallel processing multiview deconvolution tool selection Biology (General) QH301-705.5 |
| spellingShingle |
light-sheet image analysis parallel processing multiview deconvolution tool selection Biology (General) QH301-705.5 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 Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis |
| description |
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. |
| format |
article |
| author |
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 |
| author_facet |
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 |
| author_sort |
Holly C. Gibbs |
| title |
Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis |
| title_short |
Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis |
| title_full |
Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis |
| title_fullStr |
Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis |
| title_full_unstemmed |
Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis |
| title_sort |
navigating the light-sheet image analysis software landscape: concepts for driving cohesion from data acquisition to analysis |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/7b9c40c88b904acc819188e096001d6f |
| work_keys_str_mv |
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