Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis
Authors
Keywords
-
Journal
Frontiers in Cell and Developmental Biology
Volume 9, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2021-11-01
DOI
10.3389/fcell.2021.739079
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data
- (2021) Christian Tischer et al. BIOINFORMATICS
- Passive Clearing and 3D Lightsheet Imaging of the Intact and Injured Spinal Cord in Mice
- (2021) Dylan A. McCreedy et al. Frontiers in Cellular Neuroscience
- Tissue clearing and its applications in neuroscience
- (2020) Hiroki R. Ueda et al. NATURE REVIEWS NEUROSCIENCE
- Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes
- (2020) Björn Eismann et al. JOURNAL OF CELL SCIENCE
- Rapid image deconvolution and multiview fusion for optical microscopy
- (2020) Min Guo et al. NATURE BIOTECHNOLOGY
- Array programming with NumPy
- (2020) Charles R. Harris et al. NATURE
- A versatile and customizable low-cost 3D-printed open standard for microscopic imaging
- (2020) Benedict Diederich et al. Nature Communications
- Deep-learning super-resolution light-sheet add-on microscopy (Deep-SLAM) for easy isotropic volumetric imaging of large biological specimens
- (2020) Fang Zhao et al. Biomedical Optics Express
- Applications of Light-Sheet Microscopy in Microdevices
- (2019) Ignacio Albert-Smet et al. Frontiers in Neuroanatomy
- Universal light-sheet generation with field synthesis
- (2019) Bo-Jui Chang et al. NATURE METHODS
- Light-Sheet Microscopy and Its Potential for Understanding Developmental Processes
- (2019) Yinan Wan et al. Annual Review of Cell and Developmental Biology
- Advances in Ex Situ Tissue Optical Clearing
- (2019) Paweł Matryba et al. Laser & Photonics Reviews
- Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues
- (2019) Adam K. Glaser et al. Nature Communications
- BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples
- (2019) David Hörl et al. NATURE METHODS
- Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0
- (2019) Venkatakaushik Voleti et al. NATURE METHODS
- Imaging Enhancement of Light-Sheet Fluorescence Microscopy via Deep Learning
- (2019) Chen Bai et al. IEEE PHOTONICS TECHNOLOGY LETTERS
- Putting advanced microscopy in the hands of biologists
- (2019) Rory M. Power et al. NATURE METHODS
- CLIJ: GPU-accelerated image processing for everyone
- (2019) Robert Haase et al. NATURE METHODS
- Deconvolution of light sheet microscopy recordings
- (2019) Klaus Becker et al. Scientific Reports
- LITE microscopy: Tilted light-sheet excitation of model organisms offers high resolution and low photobleaching
- (2018) Tanner C. Fadero et al. JOURNAL OF CELL BIOLOGY
- Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging
- (2018) Manish Kumar et al. OPTICS EXPRESS
- Measure and model a 3-D space-variant PSF for fluorescence microscopy image deblurring
- (2018) Yemeng Chen et al. OPTICS EXPRESS
- Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms
- (2018) Tsung-Li Liu et al. SCIENCE
- Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb
- (2018) Carsten Wolff et al. eLife
- Content-aware image restoration: pushing the limits of fluorescence microscopy
- (2018) Martin Weigert et al. NATURE METHODS
- Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets
- (2018) Edouard A. Hay et al. PLoS Computational Biology
- Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy
- (2017) Yicong Wu et al. Nature Communications
- Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos
- (2016) Johannes Stegmaier et al. DEVELOPMENTAL CELL
- Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms
- (2016) Loïc A Royer et al. NATURE BIOTECHNOLOGY
- Real-time multi-view deconvolution: Fig. 1.
- (2015) Benjamin Schmid et al. BIOINFORMATICS
- Clarifying Tissue Clearing
- (2015) Douglas S. Richardson et al. CELL
- Guide to light-sheet microscopy for adventurous biologists
- (2015) Emmanuel G Reynaud et al. NATURE METHODS
- BigDataViewer: visualization and processing for large image data sets
- (2015) Tobias Pietzsch et al. NATURE METHODS
- Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms
- (2015) Matthew B. Bouchard et al. Nature Photonics
- Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool
- (2015) Abdel Aziz Taha et al. BMC MEDICAL IMAGING
- Light-sheet microscopy using an Airy beam
- (2014) Tom Vettenburg et al. NATURE METHODS
- Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data
- (2014) Fernando Amat et al. NATURE METHODS
- Efficient Bayesian-based multiview deconvolution
- (2014) Stephan Preibisch et al. NATURE METHODS
- Extensible visualization and analysis for multidimensional images using Vaa3D
- (2014) Hanchuan Peng et al. Nature Protocols
- Dual-view plane illumination microscopy for rapid and spatially isotropic imaging
- (2014) Abhishek Kumar et al. Nature Protocols
- Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
- (2014) Bi-Chang Chen et al. SCIENCE
- Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy
- (2013) Yicong Wu et al. NATURE BIOTECHNOLOGY
- OpenSPIM: an open-access light-sheet microscopy platform
- (2013) Peter G Pitrone et al. NATURE METHODS
- ImgLib2—generic image processing in Java
- (2012) Tobias Pietzsch et al. BIOINFORMATICS
- Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy
- (2012) Raju Tomer et al. NATURE METHODS
- Deep and fast live imaging with two-photon scanned light-sheet microscopy
- (2011) Thai V Truong et al. NATURE METHODS
- Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination
- (2011) Thomas A Planchon et al. NATURE METHODS
- Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans
- (2011) Y. Wu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Software for bead-based registration of selective plane illumination microscopy data
- (2010) Stephan Preibisch et al. NATURE METHODS
- CATMAID: collaborative annotation toolkit for massive amounts of image data
- (2009) S. Saalfeld et al. BIOINFORMATICS
- Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy
- (2008) P. J. Keller et al. SCIENCE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started