Neuroscientist Andreas Schaefer is spearheading a new project to capture the intricacies of the mouse brain using X-rays, bringing researchers closer to a complete map of its neural connections.
No bigger that a small bean, the mouse brain contains millions of neurons, linked by hundreds of billions of connections, collectively known as the ‘connectome’. Understanding which cells connect is key to understanding how the structure of the brain generates behaviour and cognition, and how this is impacted in diseases affecting the brain.
Mapping these connections is no easy task, but in 2024, a team in Cambridge reported that they had successfully mapped the adult fruit fly brain, less than a tenth of a cubic mm in size. In 2025, researchers at the Allen Institute in the US, completed another major project, mapping all the neurons in a 1mm3 section of a mouse brain.
A whole mouse brain is 500 times larger. So, could researchers ever produce an entire mouse connectome?
Andreas Schaefer, head of the Sensory Circuits and Neurotechnology Laboratory at the Francis Crick Institute, is pushing the boundaries of current technology to get closer to this goal.
“A technique called volume electron microscopy – where electrons are fired at a small section of a sample, and then the resulting images are built back into a 3D structure – is the gold standard for these kinds of wiring maps, like the fruit fly connectome,” he says. “But electrons can only penetrate a small sample of tissue, which has to be spliced into sections. This not only destroys the samples but also means it is very, very challenging to image bigger samples of tissue, like a full mouse brain.”
In 2020, an international team of researchers pioneered a new technique to map brain tissue, which might be less destructive and allow bigger samples to be imaged. It uses X-rays instead of electrons, as X-rays can penetrate deeper into bigger pieces of biological material. Andreas and Carles Bosch Pinol at the Crick, together with collaborators Ana Diaz and Adrian Wanner at the Paul-Scherrer Institute and the European Synchrotron, became interested in using X-rays, working to fine-tune how samples are prepared for the new imaging technique.
“Because X-rays can cause damage, we embedded tissue in radiation-proof resin, allowing us to expose samples to 20 times more radiation than if they’d been prepared using volume EM protocol,” Andreas explains. “This got us to a resolution that exposed mouse brain circuitry, including synapses and dendrites.”
This new technique involved the use of a ‘synchrotron’ – a particle accelerator that fires electrons at very high speeds through magnets to produce wavelengths of light, including X-rays – at the European Synchrotron Radiation Facility (ESRF). And the ESRF has now been upgraded to a new high-energy synchrotron, which Andreas is hoping will accelerate his goal of mapping the mouse brain.
Along with Chris Jacobsen at Northwestern University, Andreas is leading a new project to optimise sample preparation and post-imaging analysis to make use of this new powerful synchrotron. Supported by a grant from the National Institutes of Health, Andreas and Chris will work closely with Alexandra Pacureanu and Peter Cloetens at the ESRF to acquire images of large pieces of mouse brain tissue, as high resolution as possible, as quickly as possible. Chris will use supercomputers to harness the huge amounts of data and reconstruct 3D images from the X-ray imaging.
“We’re aiming to obtain sub-20 nanometre resolution in multiple millimetre volumes of mouse brain tissue,” says Andreas. “We think that, in a few years, this technique could actually get us to the entire mouse brain.”
Connectomics is currently an expensive and time-consuming endeavour, not easily accessible to researchers who could benefit from insights from the field. Part of the new grant involves widening access to connectomics through the development of the new X-ray technique.
“Once we’ve established this protocol, other research groups can come to the ESRF to use the new synchrotron,” says Andreas. “And, as other synchrotron facilities establish this ‘fourth-generation’ imaging, we’re hoping doors will open for researchers to ask questions about how connections are made in the brain, in mice, and maybe one day, humans.”
Andreas’s grant sits under the NIH’s BRAIN CONNECTS program, a global effort to comprehensively map neural connections in both humans and animals, using a variety of different imaging methods.
