SLICE Light Sheet Microscope

Neuroscience is where SLICE was born and where it does its most distinctive work. The SLICE architecture was developed specifically to image large, intact neural tissue at the resolution and scale that connectomics, circuit tracing, and whole-brain mapping demand.

SLICE images entire cleared mouse brains and spinal cords in 3D at sub-cellular resolution, with the field of view and penetration depth to map neural circuits, trace axonal projections, and identify cellular populations across whole organs. Automatic refractive index compensation means you can use whichever clearing protocol your lab has standardized on — iDISCO, CLARITY, CUBIC, BINAREE — without reconfiguring the instrument.

Where SLICE becomes a complete neuroscience workflow, not just an imaging tool, is in its native pipelines to MBF Bioscience's analysis suite. BrightSLICE exports directly into NeuroInfo for brain atlas registration and AI-driven cell quantification, Neurolucida 360 for neuron and vessel reconstruction, Stereo Investigator for unbiased stereology, and NeuroDeblur for deconvolution. No file conversion, no third-party middleware. The path from cleared brain to quantified, atlas-registered data runs through a single ecosystem.

Researchers at Columbia, Stanford, Johns Hopkins, UCSD, Harvard, and dozens of other institutions are using SLICE for whole-brain imaging, dopaminergic network mapping, vascular reconstruction, c-Fos activity screening, and developmental neurobiology. The images throughout this page — from the Tomer Lab's human vasculature work to the FosTRAP whole-brain mapping to the Kowalko Lab's cavefish brains at Lehigh — were all acquired on SLICE.

Understanding the tumor microenvironment in three dimensions — spatial organization of tumor cells, immune infiltration, vasculature, drug penetration — requires imaging that goes beyond what 2D sections and confocal stacks can provide. SLICE brings light sheet microscopy to cancer research at a price point and form factor that makes it practical for individual labs, not just core facilities.

Image cleared tumor biopsies, patient-derived organoids, and tumor spheroids at sub-cellular resolution across their full 3D volume. Track drug distribution and cellular response within intact 3D cancer models. Quantify tumor volume changes, cellular morphology, protein expression, and phenotypic shifts in response to therapies. SLICE's minimal photobleaching supports extended time-lapse imaging of live tumor dynamics — migration, invasion, angiogenesis, immune cell infiltration — without compromising sample viability.

The benchtop form factor means SLICE can be installed in containment labs and biosafety environments where floor-standing light sheet systems cannot go. BrightSLICE's wavelet compression keeps terabyte-scale screening datasets manageable, and native pipelines into MBF Bioscience's analysis suite connect imaging directly to quantification without manual data conversion.

Developmental biology and tissue engineering share a common imaging challenge: visualizing how complex 3D structures form, differentiate, and organize over time, often in samples that are delicate, irregularly shaped, or difficult to clear uniformly. SLICE's combination of gentle illumination, broad clearing-method compatibility, and sub-cellular resolution makes it well suited to both fields.

For developmental biologists, SLICE images whole embryos, developing organs, and organoids at the resolution needed to track cell populations, map gene expression patterns, and follow morphogenetic processes across intact specimens. The images on this page include a day 14.5 mouse embryo cleared with iDISCO and stained for serotonin, showing organ-level architecture and neurodevelopmental detail in a single acquisition.

For tissue engineers, SLICE enables high-resolution 3D characterization of scaffolds, engineered constructs, and vascularization patterns. Image cell-biomaterial interactions, quantify vascular density and matrix deposition, and screen multiple scaffold designs or culture conditions efficiently using SLICE's rapid volumetric acquisition. BrightSLICE handles the full pipeline from acquisition through visualization, and exported data flows directly into MBF's analysis tools or into open-source environments via OME-TIFF.