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Clearing and staining protocols


Microscope companies have responded to the popularity of cleared tissue imaging by designing optics and instrumentation to fully take advantage of the technique. The most accessible upgrades are objectives with long working distance (LWD) and cleared tissue media index of refraction matching lenses.

Leica Sp8 Laser Scanning Confocal with AOBS, White-Light Laser (WLL), and Resonant Scanner

Our Leica Sp8 was designed to be an optimal laser scanning confocal microscope for large volume cleared tissue imaging.

Nikon A1r Laser Scanning Confocal with Galvo and Resonant Scanner and

The Nikon A1r in the BIDC was built to be primarily an intra-vital multi-photon microscope, but found favor with the cleared tissue community.

Leica Thunder Imager with Computational Clearing and Deconvolution

The Thunder Imager is a widefield system, which means it is fast compared to a laser scanning confocal microscope.

Custom Homebuilt Selective-Plane Imaging Microscope (SPIM) with High-Magnification LWD Objective

This microscope build was sponsored by ImmunoX to expand the capabilities and increase the speed of acquisition for large volume cleared tissue imaging. Unfortunately, this project hit a standstill during the pandemic.


Analysis Workstations with i9 Processors, Large Amounts of RAM, Large SSDs, and an Acceptional GPU.

Our Analysis Stations #2 and #3 were designed with the large volume of data collected during cleared tissue imaging in mind.

Imaris with GPU Accelerated Display and Computation