Imagine being able to see through an entire mouse brain, witnessing the intricate dance of neurons and blood vessels in perfect clarity, or peering deep inside a human tumor to understand its unique architecture. What sounds like science fiction is now a powerful reality thanks to two revolutionary techniques: tissue clearing and light sheet microscopy.
Our bodies, and those of all animals, evolved to be opaque for good reason. Tissues are naturally packed with lipids – fatty molecules that help cells maintain their structure and function. While essential for life, these lipids scatter light, making it impossible to see deep inside organs with traditional microscopy. For over a century, scientists were limited to studying thin tissue slices, trying to reconstruct three-dimensional understanding from two-dimensional snapshots.
But what if we could make tissue transparent while keeping its structural integrity intact?
This is exactly what tissue clearing achieves. Think of a piece of tissue like a dense forest – light can’t penetrate very far because it’s blocked by countless obstacles. Tissue clearing is like carefully removing the foliage while keeping every tree trunk and branch exactly where it was, then filling the space with something that lets light pass through unimpeded.
Different clearing methods accomplish this in unique ways:
Each method has its strengths, much like different tools in a toolbox. A neuroscientist studying mouse brain circuitry might choose CLARITY for its excellent structural preservation, while a cancer researcher examining human tumors might opt for SHANEL.
Making tissue transparent was only half the battle. Traditional microscopes weren’t designed to image large cleared samples effectively. Enter light sheet microscopy – a technique that transformed how we illuminate and observe cleared tissues.
Instead of shining light through the entire sample as in traditional microscopy, light sheet microscopy illuminates just one thin plane at a time with a sheet of laser light. Imagine taking a flashlight and turning its beam into a thin, flat sheet of light – that’s essentially what light sheet microscopy does. This approach brings several remarkable advantages:
Tissue clearing is a chemical technique to make biological tissues transparent to allow for high resolution microscopic imaging of structures deep within the specimen without sectioning the tissue into thinner slices. The advantage of this is that the specimen retains its original structure and cytoarchitecture allowing researchers to investigate spatial relationships between structures, cells, and/or molecules. This is particularly valuable in research investigations involving long neural projections, vasculature, and airways. Connectomics research has been advanced significantly through the utilization of tissue clearing methods to map neural networks and trace projections.
There are a wide variety of tissue clearing methods but in general clearing a tissue specimen involves fixating objects of interest such as neurons, microvessels, and proteins while removing light-scattering molecules such as lipids to improve transparency of the specimen. Molecular labelling is then used to attach fluorophores to objects of interest for fluorescent imaging with laser microscopy tools. Lastly, the specimen is submerged in a liquid media with a specific refractive index matched to the imaging technique being utilized to scan the specimen. The final product is a semi-transparent specimen that retains the original structure and cytoarchitechture of the original organism.
Tissue clearing is being used extensively to image and quantify neural networks, dendritic spines, axonal projections between nuclei, and vascular networks in the kidney, lungs, cardiovascular system and lymphatic system. Obtaining specimen transparency is only one of the challenges faced by scientific researchers. There are technological limitations such as the maximum size of specimens that can be imaged, the enormous amount of image data collected when scanning a specimen, challenges in reconstructing large image volumes precisely, and in quantifying objects of interest to an investigation. Watch a video of a 3D Whole Brain Reconstruction Acquired with LSTM.
The combination of tissue clearing and light sheet microscopy has opened new frontiers across biological research:
In Neuroscience
Researchers can now trace neural circuits through entire brains, mapping connections that were previously impossible to visualize. This has led to groundbreaking discoveries about how different brain regions communicate and how neural networks process information.
In Cancer Research
Scientists can examine entire tumors and their surrounding environment, understanding how cancer cells interact with blood vessels and immune cells in three dimensions. This provides crucial insights for developing more effective treatments.
In Developmental Biology
Watching how organs form and tissues develop has taken on new clarity. Researchers can observe the intricate processes of embryonic development with unprecedented detail.
Successfully imaging cleared tissue requires careful choreography of sample preparation, clearing, labeling, and imaging. Each step builds on the previous one:
As these techniques continue to evolve, we’re seeing exciting new developments:
What makes tissue clearing and light sheet microscopy so powerful is not just the ability to see deeper into tissues, but the new questions this ability lets us ask. We can now study biological processes in their natural three-dimensional context, understanding spatial relationships that were previously hidden from view.
Whether you’re a neuroscientist mapping brain circuits, a cancer researcher studying tumor development, or a cell biologist exploring tissue architecture, these techniques offer unprecedented windows into the microscopic world. They remind us that sometimes the most significant scientific advances come not from seeing something entirely new, but from seeing familiar things in entirely new ways.
After capturing your cleared tissue images, the real work of discovery begins. MBF Bioscience provides a comprehensive suite of software tools designed specifically for analyzing complex 3D datasets from cleared tissue. Each tool serves a unique purpose in your research workflow:
Transform your large-scale imaging data into quantifiable insights with NeuroInfo, our advanced solution for brain-wide analysis.
Key Capabilities
Perfect For
How It Works
NeuroInfo seamlessly aligns your cleared tissue data with standard brain atlases, automatically identifying key brain regions and quantifying cells or markers within each area. This transforms months of manual analysis into automated workflows that complete in hours.
The gold standard in neuron reconstruction and analysis, Neurolucida 360 brings powerful capabilities to cleared tissue research.
Key Capabilities
Perfect For
How It Works
Neurolucida 360’s AI-powered tools automatically detect and trace neurons, spines, and vessels in your cleared tissue data. Sophisticated algorithms analyze morphology, providing detailed metrics about branch patterns, spine distributions, and network connectivity.
Turn qualitative observations into quantitative data with the industry standard in stereological analysis.
Key Capabilities
Perfect For
How It Works
Stereo Investigator applies proven stereological principles to 3D datasets, ensuring unbiased quantification of cellular populations and structures throughout your cleared tissue samples.
Optimize your cleared tissue images with our advanced deconvolution software designed specifically for light sheet microscopy data.
Key Capabilities
Perfect For
How It Works
NeuroDeblur uses sophisticated algorithms optimized for light sheet microscopy to remove blur and enhance detail in your images, revealing fine structures that might otherwise be hidden.
The true power of MBF Bioscience’s tools lies in their seamless integration:
1. Acquisition to Analysis
2. Flexible Workflows
3. Data Sharing
Whole Brain Analysis
Vascular Studies
Cell Distribution Studies
Expert Training
Technical Support
Research Community
Every research question is unique. Our team of scientists is ready to help you determine the optimal combination of tools for your specific needs. Want to explore how tissue clearing and light sheet microscopy could advance your research? Contact us to discuss your specific applications and needs.
