descSPIM : affordable but versatile light-sheet microscopy system for tissue clearing end users
descSPIM is a lightsheet microscopy system that we designed to meet the unmet needs of researchers who are using tissue clearing techniques. The system offers a low-cost and easy-to-use solution for 3D imaging of cleared tissue samples that requires little expertise and cost. Most optical components are readily available from a single vendor and can be readily assembled using the instructions provided. These minimal optical parts are arranged on a small optical breadboard. In contrast to existing lightsheet systems, descSPIM is intended to be simple to install, build, and operate, even for end users with no prior experience in optics. descSPIM is also highly expandable and can be customized to suit a variety of applications, making it a versatile tool for a wide range of research projects. With descSPIM, researchers can easily achieve practical-quality 3D imaging of cleared specimens in a daily experiments.
The main features of descSPIM are:
✓ Easy-to-build
✓ Easy-to-operate (use a cuvette / no oil chamber)
✓ Affordable ($20k-50k for descSPIM-basic, depending on the number of lasers)
✓ Compact (all parts on a 300 mm x 450 mm breadboard)
✓ Versatile (highly expandable and customizable)
Researchers interested in using Light-sheet fluorescence microscopy (LSFM) for cleared tissue imaging
・Macro- to meso-scale imaging of 3D volumetric samples prepared by tissue clearing techniques with strong efficiency (CUBIC, BABB, DISCO, SHIELDs etc.)
・Visualization of cell populations or anatomical structures (e.g. blood vessels, plaques) with cellular to sub-cellular resolutions
It is recommended to start learning Basic of optics
and Cleared sample preparation,
then to introduce descSPIM-basic.
Add-on functions are developed to be compatible with the basic system.
Add-ons: (under construction)
Related codes can be found here:
- For general data processing -> Data processing
- For false colored HE (hematoxylin & eosin) 3D converting -> Fluo-HE
- For drug distrubution analysis using trastuzumab-DyLightTM 650 -> DrugDistributionAnalysis
Note
We only tested the codes python 3.9.16 on Ubuntu 20.04 environment.
Registration was performed using ANTs software (v2.4.3.post10-g871cad0).
You can see answers for Frequently Asked Questions here.
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
By using descSPIM, you agree to abide by these terms and conditions:
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This system is only available for academic use. Any use for commercial purposes is strictly prohibited, unless permission is granted by the authors.
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Academic users are allowed to use, apply, and adopt the system in accordance with the CC by 4.0 license policy. This includes modifications, adaptations, and redistribution of the system and its components.
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If any commercial enterprise wants to use, produce, or sell the system, they must contact the authors (suishess-kyu@umin.ac.jp) to request permission.
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All users of the system must acknowledge and refer to the original paper (Otomo et al. bioRxiv 2023) in any publications or presentations resulting from the use of the system.
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The authors are not responsible for any consequences arising from the use of this system as well as related tools, scripts, and software. Users assume all risks and liabilities associated with the use.
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The authors reserve the right to modify or terminate the system and its services at any time, without prior notice.
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Users agree to comply with all applicable laws and regulations regarding the use of the system.
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Any disputes arising from the use of this system shall be resolved through negotiation between the parties. If a resolution cannot be reached, the dispute shall be submitted to binding arbitration in accordance with the laws of Japan.