Analyzing cleared tissue samples

Clearing methods are improving and our visualization and analytical tools are ready

Tissue clearing techniques have been in use since the early 1900s¹, but many of these clearing solutions deform tissue or quench fluorescence². New clearing methods such as CLARITY, 3DISCO, Sca/e, and SeeDB work with many types of fluorescent dyes that are commonly used to visualize microstructures in the brain. This is an exciting step towards an amazing goal: visualizing and analyzing complete neuronal pathways in a whole brain.

Volume rendering of mouse cerebral cortex and hippocampus. Adult Thy1-YFP-H line mouse brain was cleared with SeeDB and imaged using two-photon microscopy. Imaging area shown is 4 x 5 mm (8 x 10 tiles), 2mm thick.

Image courtesy of Dr. Takeshi Imai from PRESTO, Japan Science and Technology Agency, Saitama, Japan

Neurolucida 360

Trace and analyze neurons through the extremely large images that are a result of imaging whole mouse brains and thick tissue specimens. Neurolucida 360 helps answer questions such as: Where does this axon project to? How long is it?
In the Nature paper describing the SeeDB tissue clearing protocol, the authors used Neurolucida to trace and analyze the near-complete wiring diagram of mitral cell dendrites. The whole-mount olfactory bulb sample was too thick even with two-photon microscopy, but after clearing the tissue with their new SeeDB solution the authors were able to complete their analysis.

+ Read the published paper in Nature

+ Read a summary of the paper on our blog

Stereo Investigator

Obtain unbiased estimates of the number of cells in a region of interest, or quantify length and area. Stereo Investigator helps answer questions such as: How many cells are in the hippocampus of my specimens? What is the total volume of amyloid plaques? What is the spatial distribution of astrocytes in the temporal lobe?


Imaging whole mouse brains and thick tissue specimens yields extremely large image files that will take up valuable space on a server or hard drive – if there is even enough space for the images. Biolucida lets you quickly and easily view, organize, and share 3D images of cleared brains. Since Biolucida is compatible with Neurolucida and Stereo Investigator, you can keep all of your analysis data on Biolucida in addition to your image data. Also, this compatibility means that you can analyze any image stored on Biolucida from any computer or laptop with Neurolucida or Stereo Investigator.

There are a number of different techniques to clear tissue. This chart shows the similarities and differences between some of the more popular tissue clearing methods. Contact us to discuss which technique is best for your research question.

Quick overview of tissue clearing techniques by MBF Bioscience

¹Spalteholz, W. Über das Durchsichtigmachen von menschlichen und tierischen Präparaten. S. Hierzel. (1914).
²Hama, H. et. al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14, 1481-1489 (2011).