Efficient processing and analysis of large-scale light-sheet microscopy data

2015 ◽  
Vol 10 (11) ◽  
pp. 1679-1696 ◽  
Author(s):  
Fernando Amat ◽  
Burkhard Höckendorf ◽  
Yinan Wan ◽  
William C Lemon ◽  
Katie McDole ◽  
...  
Keyword(s):  
Large Scale ◽  
Light Sheet ◽  
Light Sheet Microscopy ◽  
Efficient Processing ◽  
Microscopy Data

scholarly journals Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution

2017 ◽  
Author(s):  
Hao Wang ◽  
Qingyuan Zhu ◽  
Lufeng Ding ◽  
Yan Shen ◽  
Chao-Yu Yang ◽  
...  
Keyword(s):  
Brain Mapping ◽  
High Speed ◽  
Large Scale ◽  
Light Sheet ◽  
Volumetric Imaging ◽  
Tissue Sections ◽  
Light Sheet Microscopy ◽  
Cell Type Specific ◽  
Microscopy Method ◽  
Immunofluorescence Labeling

We describe a new light-sheet microscopy method for fast, large-scale volumetric imaging. Combining synchronized scanning illumination and oblique imaging over cleared, thick tissue sections in smooth motion, our approach achieves high-speed 3D image acquisition of an entire mouse brain within 2 hours, at a resolution capable of resolving synaptic spines. It is compatible with immunofluorescence labeling, enabling flexible cell-type specific brain mapping, and is readily scalable for large biological samples such as primate brain.

scholarly journals An orthotopic glioblastoma animal model suitable for high-throughput screenings

2018 ◽  
Vol 20 (11) ◽  
pp. 1475-1484 ◽  
Author(s):  
Linda Pudelko ◽  
Steven Edwards ◽  
Mirela Balan ◽  
Daniel Nyqvist ◽  
Jonathan Al-Saadi ◽  
...  
Keyword(s):  
Drug Discovery ◽  
High Throughput ◽  
Large Scale ◽  
Light Sheet ◽  
Time Lapse ◽  
Zebrafish Model ◽  
Light Sheet Microscopy ◽  
Disease Biology ◽  
Vertebrate Model

Abstract Background Glioblastoma (GBM) is an aggressive form of brain cancer with poor prognosis. Although murine animal models have given valuable insights into the GBM disease biology, they cannot be used in high-throughput screens to identify and profile novel therapies. The only vertebrate model suitable for large-scale screens, the zebrafish, has proven to faithfully recapitulate biology and pathology of human malignancies, and clinically relevant orthotopic zebrafish models have been developed. However, currently available GBM orthotopic zebrafish models do not support high-throughput drug discovery screens. Methods We transplanted both GBM cell lines as well as patient-derived material into zebrafish blastulas. We followed the behavior of the transplants with time-lapse microscopy and real-time in vivo light-sheet microscopy. Results We found that GBM material transplanted into zebrafish blastomeres robustly migrated into the developing nervous system, establishing an orthotopic intracranial tumor already 24 hours after transplantation. Detailed analysis revealed that our model faithfully recapitulates the human disease. Conclusion We have developed a robust, fast, and automatable transplantation assay to establish orthotopic GBM tumors in zebrafish. In contrast to currently available orthotopic zebrafish models, our approach does not require technically challenging intracranial transplantation of single embryos. Our improved zebrafish model enables transplantation of thousands of embryos per hour, thus providing an orthotopic vertebrate GBM model for direct application in drug discovery screens.

scholarly journals Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images

2014 ◽  
Vol 30 (17) ◽  
pp. i587-i593 ◽  
Author(s):  
Paolo Frasconi ◽  
Ludovico Silvestri ◽  
Paolo Soda ◽  
Roberto Cortini ◽  
Francesco S. Pavone ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Large Scale ◽  
Light Sheet ◽  
Brain Cells ◽  
Automated Identification ◽  
Light Sheet Microscopy ◽  
Microscopy Images

scholarly journals Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution

2018 ◽  
Author(s):  
Ruixuan Gao ◽  
Shoh M. Asano ◽  
Srigokul Upadhyayula ◽  
Pisarev Igor ◽  
Daniel E. Milkie ◽  
...  
Keyword(s):  
Neural Development ◽  
High Speed ◽  
Large Scale ◽  
Neural Circuits ◽  
Light Sheet ◽  
Synaptic Proteins ◽  
Light Sheet Microscopy ◽  
Mouse Cortex ◽  
Molecular Contrast ◽  
The Brain

AbstractOptical and electron microscopy have made tremendous inroads in understanding the complexity of the brain, but the former offers insufficient resolution to reveal subcellular details and the latter lacks the throughput and molecular contrast to visualize specific molecular constituents over mm-scale or larger dimensions. We combined expansion microscopy and lattice light sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain, including synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly neuropil domain. The technology should enable statistically rich, large scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.One Sentence SummaryCombined expansion and lattice light sheet microscopy enables high speed, nanoscale molecular imaging of neural circuits over large volumes.

scholarly journals Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution

Science ◽  
2019 ◽  
Vol 363 (6424) ◽  
pp. eaau8302 ◽  
Author(s):  
Ruixuan Gao ◽  
Shoh M. Asano ◽  
Srigokul Upadhyayula ◽  
Igor Pisarev ◽  
Daniel E. Milkie ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Neural Development ◽  
Dopaminergic Neurons ◽  
Large Scale ◽  
Light Sheet ◽  
Synaptic Proteins ◽  
Light Sheet Microscopy ◽  
Mouse Cortex ◽  
Molecular Contrast ◽  
The Brain

Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entireDrosophilabrain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

scholarly journals Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging

2019 ◽  
Author(s):  
Tonmoy Chakraborty ◽  
Meghan Driscoll ◽  
Malea Murphy ◽  
Philippe Roudot ◽  
Bo-Jui Chang ◽  
...  
Keyword(s):  
Dendritic Spines ◽  
Large Scale ◽  
Light Sheet ◽  
Automated Detection ◽  
Field Of View ◽  
Large Field ◽  
Axial Resolution ◽  
Optical Sectioning ◽  
Isotropic Resolution ◽  
Light Sheet Microscopy

AbstractWe present cleared tissue Axially Swept Light-Sheet Microscopy (ctASLM), which achieves sub-micron isotropic resolution, high optical sectioning capability, and large field of view imaging (870×870 μm2) over a broad range of immersion media. ctASLM can image live, expanded, and both aqueous and organic chemically cleared tissue preparations and provides 2- to 5-fold better axial resolution than confocal or other reported cleared tissue light-sheet microscopes. We image millimeter-sized tissues with sub-micron 3D resolution, which enabled us to perform automated detection of cells and subcellular features such as dendritic spines.

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