Low cost light-sheet microscopy for whole brain imaging

Manish Kumar, Jordan Nasenbeny, Yevgenia Kozorovitskiy

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


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
ISBN (Electronic)9781510614833
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
ISSN (Print)1605-7422


ConferenceThree-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV 2018
CountryUnited States
CitySan Francisco


  • 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

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