Low cost light-sheet microscopy for whole brain imaging

Manish Kumar, Jordan Nasenbeny, Yevgenia Kozorovitskiy

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Light-sheet microscopy has evolved as an indispensable tool in imaging biological samples. It can image 3D samples at fast speed, with high-resolution optical sectioning, and with reduced photobleaching effects. These properties make light-sheet microscopy ideal for imaging fluorophores in a variety of biological samples and organisms, e.g. zebrafish, drosophila, cleared mouse brains, etc. While most commercial turnkey light-sheet systems are expensive, the existing lower cost implementations, e.g. OpenSPIM, are focused on achieving high-resolution imaging of small samples or organisms like zebrafish. In this work, we substantially reduce the cost of light-sheet microscope system while targeting to image much larger samples, i.e. cleared mouse brains, at single-cell resolution. The expensive components of a lightsheet system - excitation laser, water-immersion objectives, and translation stage - are replaced with an incoherent laser diode, dry objectives, and a custom-built Arduino-controlled translation stage. A low-cost CUBIC protocol is used to clear fixed mouse brain samples. The open-source platforms of μManager and Fiji support image acquisition, processing, and visualization. Our system can easily be extended to multi-color light-sheet microscopy.

Original languageEnglish (US)
Title of host publicationThree-Dimensional and Multidimensional Microscopy
Subtitle of host publicationImage Acquisition and Processing XXV
EditorsTony Wilson, Carol J. Cogswell, Thomas G. Brown
PublisherSPIE
Volume10499
ISBN (Electronic)9781510614833
DOIs
StatePublished - Jan 1 2018
EventThree-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV 2018 - San Francisco, United States
Duration: Jan 29 2018Jan 31 2018

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
Volume10499
ISSN (Print)1605-7422

Conference

ConferenceThree-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV 2018
CountryUnited States
CitySan Francisco
Period1/29/181/31/18

Fingerprint

Neuroimaging
brain
Microscopy
Brain
Microscopic examination
microscopy
Imaging techniques
Light
Costs and Cost Analysis
mice
Costs
Zebrafish
organisms
Fiji
Photobleaching
Semiconductor Lasers
resolution cell
Laser excitation
water immersion
Fluorophores

Keywords

  • Brain
  • Fluorescence imaging
  • Light-sheet microscopy
  • Low-cost microscopy

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging

Cite this

Kumar, M., Nasenbeny, J., & Kozorovitskiy, Y. (2018). Low cost light-sheet microscopy for whole brain imaging. In T. Wilson, C. J. Cogswell, & T. G. Brown (Eds.), Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV (Vol. 10499). [104991I] (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 10499). SPIE. https://doi.org/10.1117/12.2288497
Kumar, Manish ; Nasenbeny, Jordan ; Kozorovitskiy, Yevgenia. / Low cost light-sheet microscopy for whole brain imaging. Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV. editor / Tony Wilson ; Carol J. Cogswell ; Thomas G. Brown. Vol. 10499 SPIE, 2018. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE).
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Kumar, M, Nasenbeny, J & Kozorovitskiy, Y 2018, Low cost light-sheet microscopy for whole brain imaging. in T Wilson, CJ Cogswell & TG Brown (eds), Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV. vol. 10499, 104991I, Progress in Biomedical Optics and Imaging - Proceedings of SPIE, vol. 10499, SPIE, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV 2018, San Francisco, United States, 1/29/18. https://doi.org/10.1117/12.2288497

Low cost light-sheet microscopy for whole brain imaging. / Kumar, Manish; Nasenbeny, Jordan; Kozorovitskiy, Yevgenia.

Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV. ed. / Tony Wilson; Carol J. Cogswell; Thomas G. Brown. Vol. 10499 SPIE, 2018. 104991I (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 10499).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Kumar M, Nasenbeny J, Kozorovitskiy Y. Low cost light-sheet microscopy for whole brain imaging. In Wilson T, Cogswell CJ, Brown TG, editors, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV. Vol. 10499. SPIE. 2018. 104991I. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE). https://doi.org/10.1117/12.2288497