The Complete Light Sheet Theta Microscope System for Cleared Tissue Imaging and Analysis

ClearScope is a revolutionary light sheet theta microscope system designed to work with a wide range of cleared specimens. Its patent pending technology has been developed through a collaboration between scientists at Columbia University and MBF Bioscience. ClearScope is designed to meet the unique challenges inherent to imaging cleared organs and brain specimens with high-resolution optics capable of distinguishing and obtaining quantifiable imaging data pertaining to fluorescence, neurons, vessels, and subcellular structures like dendritic spines.

ClearScope utilizes a patent pending approach called Light Sheet Theta Microscopy that provides ClearScope with important advantages over other light sheet microscopy methods:

  • Image large specimens, including tissue slabs from humans and other primates
  • Image smaller specimens, such as whole mouse and rat brains
  • Capture the details of the entire specimen with high optical resolution over an exceptionally large lateral area 
  • High speed image acquisition
  • Easy to use
  • Efficient data compression to minimize data storage requirements and maximize speed
  • Works with our acclaimed analysis software to map and trace neural structures and microvessels 
  • Compatible with all cleared tissue methods through the use of sealed specimen chambers
  • Two independent illumination pathways eliminate shadow effects and uneven illumination

Unique Advantages of Light Sheet Theta Microscopy (LTSM)

At the core of the LSTM technology is the use of two illumination pathways oblique to the specimen and detection pathway. This provides ClearScope with the ability to image thicker tissue specimens over a large lateral area (XY) at higher optical resolutions, while maintaining fast imaging speed, high imaging quality, and low photo-bleaching.

  • Stage range of motion is the only limit to specimen lateral dimensions
  • Two intersecting light sheets form an ultra-thin light sheet (2-6µm) that optimizes axial image resolution and quality, produces uniform illumination, and reduces out of focus features.
  • The oblique light sheet arrangement allows for utilization of high numerical aperture (NA) and long working distance (WD) objectives. 
  • The light sheet scans across the detection focal plane synchronized with the rolling shutter of the camera
  • The electrically tunable lens (ETL) in each arm translates the light sheet across the specimen in conjunction with the galvanometer scanner ensuring that the specimen is always illuminated using the thinnest section of the intersecting light sheets. 
  • Illumination from the intersecting light sheets doesn’t vary with increasing depth. 
  • Refractive Index (RI) correction is performed by automatically adjusting the depth of the light sheet as a function of tissue depth. This allows a single detector objective to image specimens cleared with various clearing protocols, e.g. Clarity, iDisco, etc.
  • Each light sheet configuration is individually calibrated for a given RI media and laser wavelength. Users can select the appropriate configuration file within the GUI.

ClearScope Performance Specifications

  • Maximum Imaging Depth = 12mm (working distance depends on choice of objective lens)
  • Maximum Specimen Size = 114mm x 75mm x 12mm with standard stage, virtually unlimited lateral dimensions with larger stages
  • Refractive index range = 1.38 – 1.56
  • Objective Lens Magnifications = 10x, 17x, 20x, 24x, and 25x
  • Numerical Aperture = 0.4 – 1.0NA (depends on objective lens)
  • Horizontal (XY) optical resolution = 0.35 μm (with 20x objective lens)
  • Laser wavelengths =  405 / 488 / 561 / 640 nm (customizable)
  • Specimen chambers: for whole mouse or rat brains, tissue slabs from primates, plus custom chambers available
  • Single field-of-view pixel resolution = 2048 x 2048 pixels 
  • Image digitization = 16 bit
  • Light sheet thickness = 2 - 6μm depending on optics
  • Compatible with many tissue clearing techniques including : CLARITY, iDISCO, uDISCO, SeeDB and Sca/e


ClearScope is designed to be customizable to address the specific needs of researchers in a variety of fields. To maximize effectiveness and accommodate a wide range of budgets, researchers can select the number and wavelengths of illumination lasers, number of illumination arms (1 or 2), objective lenses, and more.

System components can even be upgraded and expanded at a later time; for example, adding more laser wavelengths as needed. This makes ClearScope the most adaptable light sheet microscope system to fulfill all the needs of multiple research labs or core facilities.


Images Acquired by ClearScope

Unlike the other light sheet microscope systems on the market, ClearScope was created with automation and efficiency in mind to help researchers increase scientific thoughput without having to be an expert in optics or hardware control. With ClearScope you can collect better 3D images in substantially less time, analyze your data in far more detail, and gain much insight into your scientific investigation using ClearScope.


Observe a 3D Whole Brain Reconstruction Acquired with LSTM


Developed, Tested, and Supported by Expert Scientists

ClearScope has been developed through years of collaborative research between Raju Tomer, Ph.D. at Columbia University and MBF. As with all of our products at MBF, we work directly with academic and institutional researchers to build innovative products that support the needs of the research and medical communities. We interact with our customers and collaborators daily, continuously adding features and analyses to make sure our hardware and software products are continuously improving and stay up to date with the latest scientific discoveries. To see examples of how researchers have used Light Sheet Theta Microscopy for their own research, consult the following publication:

Migliori, B., Datta, M. S., Dupre, C., Apak, M. C., Asano, S., Gao, R., … Tomer, R. (2018). Light sheet theta microscopy for rapid high-resolution imaging of large biological samples. BMC Biology, 16(1). doi: 10.1186/s12915-018-0521-8


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