SSBD Project Detail

416-Otomo-descSPIM

Project

Title

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

Description

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.

License

CC BY

Released at

Oct. 20, 2025, midnight

Updated at

Funding

This study was supported by the Japan Agency for Medical Research and Development (AMED) PRIME (to E.A.S., grant number JP20gm6210027); AMED Research on Development of New Drugs (to A.H. and E.A.S., grant number JP21ak0101181); AMED Brain/MINDS (to E.A.S. and T.Nemoto, grant number JP21wm0425003, and JP19dm0207078); AMED Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE) (to E.A.S., grant number JP22ama221517); Japan Science and Technology Agency (JST) CREST (to K.Otomo and E.A.S., grant number JPMJCR20E4 and JPMJCR23B7); Japan Society for the Promotion of Science (JSPS) KAKENHI grant-in-aid for scientific research (B) (to K.Otomo and E.A.S., grant number JP22H02756 and JP22H02824); JSPS KAKENHI grant-in-aid for scientific research (S) (to T.Nemoto and K.Otomo, grant number JP20H05669); JSPS KAKENHI grant-in-aid for challenging research (exploratory) (to K.Otomo, grant number JP21K19346); JSPS KAKENHI grant-in-aid for transformative research areas - platforms for advanced technologies and research resources “Advanced Bioimaging Support” (to T.Nemoto and E.A.S., grant number JP22H04926); JSPS KAKENHI grant-in-aid for fund for the promotion of joint international research (Fostering Joint International Research(B)) (to K.Otomo, grant number JP22KK0100); JSPS KAKENHI for international leading research (to E.A.S., grant number JP23K20044); Operating Costs Subsidies for Private Universities (to E.A.S.); Grants-in-Aid from UTEC-UTokyo (to E.A.S.); the Takeda Science Foundation (to E.A.S.); Nakatani foundation for advancement of measuring technologies in biomedical engineering (to E.A.S.); The Mochida Memorial Foundation for Medical and Pharmaceutical Research (to E.A.S.), and The Uehara Memorial Foundation (to E.A.S.).

# of image datasets

Papers

Paper information: Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun. 2024 Jun 12;15(1):4941.,
Pubmed ID: 38866781,
PMCID: PMC11169475,
DOI: https://doi.org/10.1038/s41467-024-49131-1,
URL: https://pubmed.ncbi.nlm.nih.gov/38866781/

Contacts

Etsuo A Susaki (Contact) , Department of Biochemistry and Systems Biomedicine , Juntendo University
Kohei Otomo (Imaging Contibutor)

Biosamples

Organisms

Mus musculus (NCBI:txid10090)
Homo sapiens (NCBI:txid9606)

Strains

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

Cells

neuron (CL_0000540)

Cell lines

BT-474 cell

Ontologies

UBERON

brain (UBERON_0000955)

Anatomical entities

GO: Biological processes

GO: Cellular components

plasma membrane (GO:0005886)
nucleus (GO:0005634)
cytoplasm (GO:0005737)

GO: Molecular functions

Genetics

Gene names

Protein names

Platelet endothelial cell adhesion molecule (Q08481)

Genetic methods

transgenic (EFO_0004020)

Protein tags

Fluorescein (FITC) (FBbi:00000451)
Yellow fluorescent protein from Aequorea (FBbi:00000439)

Probes

labeled primary antibody (FBbi:00000130)

Oligo Primer

Genotype

Treatments

Reagent or Compound

Concentration

Fold Dilution

Imaging Methods

Dimensions

1500x2300x679x3x1, 2160x4096x997x2x1, 2160x4096x681x3x1, 2160x4096x679x3x1, 3862x5791x1016x2x1, 2160x4096x680x3x1, 2160x4096x682x3x1,

X scales

3.5 micrometer,

Y scales

3.5 micrometer,

Z scales

10 micrometer,

T scales

NA,

Channels

2 channel, 3 channel,

Microscopy types

fluorescence microscopy (FBbi:00000246)

Detection methods

Visualization methods

Illumination methods

Sources of contrast

Contrast enhancing methods

Resolution enhancing methods

Imaged parameters

Sample preparation methods

Instruments

Body

custom made

Model

Light source

Cobolt Skyra 488 nm and 561 nm

Detector

Thorlabs CMOS camera CS895MU

Objective

Thorlabs TL2X-SAP (NA = 0.1, WD= 56.3mm)

Filter set

Thorlabs, FBH520-40 and FBH600-40

Dichroic

Body

custom made

Model

Light source

Cobolt Skyra 488 nm, 561 nm and 647 nm

Detector

Thorlabs CMOS camera CS895MU

Objective

Thorlabs TL2X-SAP (NA = 0.1, WD= 56.3mm)

Filter set

Thorlabs, FBH520-40, FBH600-40 and FBH700-40

Dichroic

Datasets

Dataset name

Organism

Gene / Protein

Dimensions

File size

SSBD:OMERO

Download

Fig3_brain_RightAnterior_1

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_RightAnterior_2

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_RightPosterior_1

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_RightPosterior_2

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_LeftPosterior_1

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_LeftPosterior_2

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_LeftAnterior_1

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_LeftAnterior_2

Mus musculus (NCBI:txid10090)

2160x4096x997x2x1

17.6GB

zip

Fig3_brain_3Drender

Mus musculus (NCBI:txid10090)

3862x5791x1016x2x1

45.5GB

zip

Fig4_xenograft_center_1

Homo sapiens (NCBI:txid9606)