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Light Sheet Fluorescent Microscopy

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Light Sheet Capabilities at ClearLight Bio

Light Sheet Fluorescent Microscopy

In addition to CLARITY Tissue Clearing and thick tissue immunostaining ClearLight Lab Services include fluorescent microscopy and 3D image analysis. Images are acquired on either a confocal or lightsheet microscopy platform depending upon the tissue type, and the research questions involved.

Light Sheet Imaging Capabilities

ClearLight’s light sheet fluorescence microscope (LSFM), also called Selective Plane Illumination Microscopy (SPIM) is a highly capable microscope manufactured by Bruker | Luxendo. ClearLight Bio’s MuVi SPIM microscope is customized to accommodate a wide range of tissue sizes and imaging needs.

Mouse Kidney on Light Sheet Microscope

DAPI (blue), Lectin (green), RedDot™2 Far-Red Nuclear Stain (magenta)

Light Sheet Microscopy Fast Facts

  • Sample chamber can handle whole optically cleared mouse brains and other organs.
  • Unit provides fast image acquisition in a single plane of light orthogonal to the detection objective lenses, minimizing photobleaching in thick specimens.
  • Six lasers provide increased multiplex channels over the confocal image acquisition platform.
  • Luxendo LuxData comprehensive data processing and storage solution provides fast transfer and large-capacity storage to handle the large data volumes generated by the light sheet.

Advantages of Light Sheet Fluorescent Microscopy

Acquiring more of your sample with more biomarkers in less time than confocal.

Fast Image Acquisition

Imaging can be completed on the light sheet at much faster speeds compared to the time required on confocal microscopes. This means less wait time for our Lab Services clients.

Good Optical Sectioning

On a light sheet microscope, it is possible to be precise in which parts of the sample are illuminated at any one time. This allows for sharper, high contrast images, minimizing any out-of-focus fluorescence, as well as reducing the chances of photobleaching.

Low Photobleaching

Using the light sheet microscope allows us to pinpoint the excitation light only where it is needed, reducing the chances of photobleaching, especially when imaging large samples.

Larger Sample Sizes

Larger samples can be imaged on the light sheet versus confocal microscopy. For example, many of our clients wish to image whole mouse brains, which can be done on the light sheet, but not on the confocal platform due to chamber size limitations.

More Fluorescent Channels

Up to 6 biomarker channels can be imaged at one time on the light sheet microscope versus only 4 channels on the confocal microscope. More data in less time.

Imaging Data Formats

Preclinical researchers who work with ClearLight Lab Services receive imaging data in two formats, the standard 2D slice view, as played through the familiar Z stack, as well as a 3D volumetric rendering that rotates the sample. This provides critical context that cannot be seen using the gold standard 2D FFPE methods.

Fluorescent Light Sheet Microscopy Examples

This is a mouse brain imaged with a light sheet microscope.

This tissue is a section of small intestine imaged with our light sheet microscope.

This tissue is a mouse heart imaged via our light sheet microscope.

This is another look at mouse kidney on the light sheet.

Where Light Sheet Fluorescent Microscopy Fits

After tissue clearing, the tissue processing workflow moves from molecular labeling and then on to imaging. The stained tissue is placed in a refractive index-matching mounting solution for fluorescent imaging with a confocal or light sheet microscope depending upon the sample type and research goals.

Discovering Your Imaging Goals

Should you request fluorescent light sheet imaging for your projects? That depends. If your project involves spheroids the answer is probably not. You probably don’t need terabytes of data for a tonsil sample.

Appropriate Projects for Light Sheet

So what kind of projects would benefit from light sheet fluorescent microscopy? How do you decide? The good news is you don’t really have to decide. Tell us about your research goals and about your samples to be processed and we’ll recommend the best path forward.

Tell Us About Your Project

Take the first step in beginning your project:

  • What do you need to see?
  • How big is your sample?
  • Do you need to scan an entire tissue sample or is there a specific region of interest?

Is this an exploratory project meaning you don’t quite know what you are looking for yet? Or, is this a refinement project, where you are narrowing in your focus.


    Analysis can be performed for select biomarkers, please contact us to find out if your target of interest is one of them. Imaging is currently performed on select fields of view instead of the entire sample.

    Submission Guidelines

    Tissue Sample Requirements: