X-ray imaging captures the brain’s intricate connections

An international team of researchers led by the Francis Crick Institute, working with the Paul Scherrer Institute, have developed a new imaging protocol to capture mouse brain cell connections in precise detail.

In work published today in Nature Methods, they combined the use of X-rays with radiation-resistant materials sourced from the aerospace industry.

The images acquired using this technique allowed the team to see how nerve cells connect in the mouse brain, without needing to thinly slice biological tissue samples.

Volume electron microscopy (volume EM) has been the gold standard for imaging how nerve cells connect as ‘circuitry’ inside the brain. It has paved the way for scientists to create maps called connectomes, of entire brains, first in fruit fly larvae and then the adult fruit fly. This imaging involves cutting 10s of nm thin slices (tens of thousands per mm of tissue), imaging each slice and then building the images back into their 3D structure.

Compared to electrons, X-rays have the potential to penetrate deeper into the matter, so the team set out to investigate if this type of imaging would be suitable for capturing the fine details of nerve cells in tissue, without the need to slice the sample.

Building on standard volume EM sample preparation protocols, they tested a new step – embedding the stained tissue using a resin developed in the nuclear and aerospace industries. This resin can prevent nuclear reactors or spaceships from being damaged by radiation, and in this experiment, allowed the samples to be exposed to at least 20 times more radiation, reaching billions more X-rays than would be fatal for a human.

The samples were then imaged using X-rays in a large facility called a synchrotron – a ‘particle accelerator’ which uses magnetic and electric fields to propel electrons at very high speeds, which then produce intense and coherent X-ray radiation.

The resulting images, produced using a specific type of X-ray imaging called X-ray ptychography, reached a resolution of 38nm. This was enough to show multiple elements of the mouse brain circuitry, including synapses (areas where two neurons connect), dendrites (nerve cell projections), and many axons (wires carrying electrical information).

Andreas Schaefer, Principal Group Leader of the Sensory Circuits and Neurotechnology Laboratory at the Crick, said: “Volume EM has been revolutionary for seeing things inside the cell in 3D, but it comes with limitations for mapping neuron connections inside mammalian brains, which are too large to be reliably sliced into tiny sections.

“We’re excited that our protocol and use of powerful radiation-resistant material allowed brain tissue to be imaged at extraordinary resolution. Refining this technique further could bring us one small step closer to a future goal in the field: mapping the mouse brain connectome, which is tens of thousands of times bigger than the fruit fly connectome.”

Carles Bosch Piñol, Principal Laboratory Research Scientist in the Sensory Circuits and Neurotechnology Laboratory at the Crick, said: “Now we’ve shown that X-ray imaging is suitable for mapping the fine detail of delicate biological tissue samples in 3D, we’re continuing to make the methods better and better.

“We want to improve the field of view, addressing larger samples, and the resolution, obtaining finer details. Combining X-ray imaging with other methods opens up new possibilities to study the function of biological tissues such as the brain.”

The project was co-led by Ana Diaz and Adrian Wanner at the Paul Scherrer Institut (Villigen, Switzerland), and performed in collaboration with the European Synchrotron Radiation Facility and the Electron Microscopy team at the Crick.

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Notes to Editors

Reference: Bosch, C. et al. (2025). Nondestructive X-ray tomography of brain tissue ultrastructure. Nature Methods. 10.1038/s41592-025-02891-0.

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