SSBD:database

Key Organism Strain Cell Line Gene Symbol Protein name Protein tag Reporter Project ID Dataset ID Title Description Data Type Gene Ontology Biological Imaging Methods Method Summary Paper Information Medical Subject Headlines Person

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416-Otomo-descSPIM

https://ssbd.riken.jp/database/416-Otomo-descSPIM/

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ssbd-repos-000416

https://ssbd.riken.jp/repository/416/

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Images of brain and xenograft obtained by descSPIM, the desktop- equipped SPIM

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.

2025-11-28

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CC BY

Image data based on Experiment

20 ( Image datasets: 20, Quantitative data datasets: 0 )

348.6 GB ( Image datasets: 348.6 GB, Quantitative data datasets: 0 bytes )

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Homo sapiens, Mus musculus

B6.Cg-Tg(Thy1-YFP)HJrs/J

BT-474 cell

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nucleus, plasma membrane, cytoplasm

selective plane illumination microscopy (SPIM), fluorescence microscopy

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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, Satoshi Takagi, Ryohei Katayama, Yusuke Iwata, Toshiro Shiokawa, Yoku Hayakawa, Kensuke Otsuka, Haruko Watanabe-Takano, Yuka Haneda, Shigetomo Fukuhara, Miku Fujiwara, Takenobu Nii, Chikara Meno, Naoki Takeshita, Kenta Yashiro, Juan Marcelo Rosales Rocabado, Masaru Kaku, Tatsuya Yamada, Yumiko Oishi, Hiroyuki Koike, Yinglan Cheng, Keisuke Sekine, Jun-Ichiro Koga, Kaori Sugiyama, Kenichi Kimura, Fuyuki Karube, Hyeree Kim, Ichiro Manabe, Tomomi Nemoto, Kazuki Tainaka, Akinobu Hamada, Hjalmar Brismar, Etsuo A Susaki (2024) descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques., Nature communications, Volume 15, Number 1, pp. 4941

Published in 2024 Jun 12 (Electronic publication in June 12, 2024, midnight )

• doi: 10.1038/s41467-024-49131-1
• pmid: 38866781
  

(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.

(MeSH Terms)

• Animals
• Mice
• Brain/diagnostic imaging[major]
• Humans
• Microscopy, Fluorescence/methods[major]
• Microscopy, Fluorescence/instrumentation[major]
• Imaging, Three-Dimensional/methods[major]
• Cell Line, Tumor

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Etsuo A Susaki , Juntendo University , Department of Biochemistry and Systems Biomedicine , Department of Biochemistry and Systems Biomedicine

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