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descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques

Author

Listed:
  • Kohei Otomo

    (Juntendo University Graduate School of Medicine
    Juntendo University School of Medicine
    Juntendo University Graduate School of Medicine
    National Institutes of Natural Sciences)

  • Takaki Omura

    (Juntendo University Graduate School of Medicine
    Juntendo University Graduate School of Medicine
    University of Tokyo
    National Cancer Center Hospital)

  • Yuki Nozawa

    (Juntendo University School of Medicine)

  • Steven J. Edwards

    (KTH Royal Institute of Technology)

  • Yukihiko Sato

    (Juntendo University Graduate School of Medicine
    Juntendo University Graduate School of Medicine)

  • Yuri Saito

    (Juntendo University Graduate School of Medicine
    Juntendo University Graduate School of Medicine)

  • Shigehiro Yagishita

    (National Cancer Center Research Institute
    National Cancer Center Research Institute)

  • Hitoshi Uchida

    (Niigata University)

  • Yuki Watakabe

    (National Institutes of Natural Sciences
    National Institutes of Natural Sciences)

  • Kiyotada Naitou

    (Kagoshima University)

  • Rin Yanai

    (National Institutes for Quantum Science and Technology)

  • Naruhiko Sahara

    (National Institutes for Quantum Science and Technology)

  • Satoshi Takagi

    (Japanese Foundation for Cancer Research)

  • Ryohei Katayama

    (Japanese Foundation for Cancer Research)

  • Yusuke Iwata

    (The University of Tokyo)

  • Toshiro Shiokawa

    (The University of Tokyo)

  • Yoku Hayakawa

    (The University of Tokyo)

  • Kensuke Otsuka

    (Central Research Institute of Electric Power Industry)

  • Haruko Watanabe-Takano

    (Institute for Advanced Medical Sciences, Nippon Medical School)

  • Yuka Haneda

    (Institute for Advanced Medical Sciences, Nippon Medical School)

  • Shigetomo Fukuhara

    (Institute for Advanced Medical Sciences, Nippon Medical School)

  • Miku Fujiwara

    (Kyushu University)

  • Takenobu Nii

    (Kyushu University)

  • Chikara Meno

    (Kyushu University)

  • Naoki Takeshita

    (Kyoto Prefectural University of Medicine
    Kyoto Prefectural University of Medicine)

  • Kenta Yashiro

    (Kyoto Prefectural University of Medicine)

  • Juan Marcelo Rosales Rocabado

    (Niigata University)

  • Masaru Kaku

    (Niigata University)

  • Tatsuya Yamada

    (University of Nebraska-Lincoln)

  • Yumiko Oishi

    (Tokyo Medical and Dental University)

  • Hiroyuki Koike

    (Tokyo Medical and Dental University)

  • Yinglan Cheng

    (Tokyo Medical and Dental University)

  • Keisuke Sekine

    (National Cancer Center Research Institute)

  • Jun-ichiro Koga

    (University of Occupational and Environmental Health)

  • Kaori Sugiyama

    (Waseda University)

  • Kenichi Kimura

    (University of Tsukuba)

  • Fuyuki Karube

    (Hokkaido University)

  • Hyeree Kim

    (Chiba University)

  • Ichiro Manabe

    (Chiba University)

  • Tomomi Nemoto

    (National Institutes of Natural Sciences
    National Institutes of Natural Sciences)

  • Kazuki Tainaka

    (Niigata University)

  • Akinobu Hamada

    (National Cancer Center Research Institute
    National Cancer Center Research Institute)

  • Hjalmar Brismar

    (KTH Royal Institute of Technology)

  • Etsuo A. Susaki

    (Juntendo University Graduate School of Medicine
    Juntendo University School of Medicine
    Juntendo University Graduate School of Medicine)

Abstract

Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000–50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.

Suggested Citation

  • Kohei Otomo & Takaki Omura & Yuki Nozawa & Steven J. Edwards & Yukihiko Sato & Yuri Saito & Shigehiro Yagishita & Hitoshi Uchida & Yuki Watakabe & Kiyotada Naitou & Rin Yanai & Naruhiko Sahara & Satos, 2024. "descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49131-1
    DOI: 10.1038/s41467-024-49131-1
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    References listed on IDEAS

    as
    1. Adam K. Glaser & Nicholas P. Reder & Ye Chen & Chengbo Yin & Linpeng Wei & Soyoung Kang & Lindsey A. Barner & Weisi Xie & Erin F. McCarty & Chenyi Mao & Aaron R. Halpern & Caleb R. Stoltzfus & Jonatha, 2019. "Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
    2. Paul R. H. J. Timmers & James F. Wilson & Peter K. Joshi & Joris Deelen, 2020. "Multivariate genomic scan implicates novel loci and haem metabolism in human ageing," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    3. Benedict Diederich & René Lachmann & Swen Carlstedt & Barbora Marsikova & Haoran Wang & Xavier Uwurukundo & Alexander S. Mosig & Rainer Heintzmann, 2020. "A versatile and customizable low-cost 3D-printed open standard for microscopic imaging," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    4. Nikita Vladimirov & Fabian F. Voigt & Thomas Naert & Gabriela R. Araujo & Ruiyao Cai & Anna Maria Reuss & Shan Zhao & Patricia Schmid & Sven Hildebrand & Martina Schaettin & Dominik Groos & José María, 2024. "Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    5. Kwanghun Chung & Jenelle Wallace & Sung-Yon Kim & Sandhiya Kalyanasundaram & Aaron S. Andalman & Thomas J. Davidson & Julie J. Mirzabekov & Kelly A. Zalocusky & Joanna Mattis & Aleksandra K. Denisin &, 2013. "Structural and molecular interrogation of intact biological systems," Nature, Nature, vol. 497(7449), pages 332-337, May.
    6. Maged Goubran & Christoph Leuze & Brian Hsueh & Markus Aswendt & Li Ye & Qiyuan Tian & Michelle Y. Cheng & Ailey Crow & Gary K. Steinberg & Jennifer A. McNab & Karl Deisseroth & Michael Zeineh, 2019. "Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI," Nature Communications, Nature, vol. 10(1), pages 1-17, December.
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