Periodic Reporting for period 1 - BioDir-X (An X-ray beam tracking approach to retrieve directional information in biological specimens)
Reporting period: 2022-09-01 to 2024-11-30
The complexity of the nervous system (NS) is mainly related to its multi-scale connectivity, from the synaptic connections up to axons and nerves. The mapping of such pathways represents the first step towards the understanding of the NS functional connectivity and its changing with aging. Currently, the gold standard for the non-invasive investigation of fiber connectivity is the magnetic resonance diffusion tensor imaging which is based on the measurement of the thermal motion of water molecules in the specimen. While it meets the requirements for clinical usage, it suffers from low resolution, typically in the range of 1-2 mm in humans and around 100 microns in animals, that is still coarse compared to the size of fibers bundles. This scale is unsuitable for high-resolution applications such as preclinical small animal imaging. In addition, the characterization of fibers direction on a micrometric scale has applications also in materials science, such as for the investigation of composites. In this case, both the absence of water in the specimen and the low resolution prevents the use of DTI, making X-ray directional imaging the only viable solution. It is worth noting that small size of the fibers requires sub-micron spatial resolution to resolve and follow them through computed tomography (CT). While this is within the capabilities of state-of-the-art laboratory micro-CT systems, it typically imposes a small field of view providing only a local description of fibres arrangement. Therefore, the availability of an X-ray technique providing directional information over a large field of view is needed. In addition, the use of incoherent or partially coherent X-ray techniques will allow an easy implementation into laboratories. In this project, we proposed the use of the X-ray beam tracking technique based on a single absorption mask to retrieve directional information from a biological specimen. This has several advantages over other X-ray techniques such as grating interferometry. Specifically, the use a single absorption mask greatly reduced the complexity of the system improving its stability and does not require a partially coherent beam as it is needed for the speckle imaging.
The project was designed with sequential tasks, with the final goal of implementing a directional beam tracking setup in the laboratory. It required the development of a simulation tool to optimize the acquisition protocol and test retrieval algorithms which was designed by exploiting the existing Monte Carlo engine MCXtrace, combined with Matlab, to create a fully automated script for simulating directional imaging experiments by rotating the sample in all required directions. A specific sample model made of carbon tubes was developed, and a simple wave optics approximation was used to describe the interaction of photons with matter. Simulations played a fundamental role in the work, allowing for the testing of retrieval algorithms and experimental parameters.
Subsequently, biological samples and phantoms were developed. For the phantoms, carbon composites were oriented in different directions and embedded in self-made epoxy resin blocks, which were then sliced using a high-speed saw into sections of about 150 microns. For the mouse brain and spinal cord, a xylene-based fixation was used for sample preparation, as it has been shown to greatly highlight fibers. These were then embedded and sliced in the same way as the phantoms.
The samples were measured during an experiment at the synchrotron with masks featuring different parameters. Simultaneously, a laboratory setup for implementing directional beam tracking was designed, including the source, the sample stage, and the X-ray detector, paving the way for additional applications we expect will extend also after the completion of the project.
Subsequently, biological samples and phantoms were developed. For the phantoms, carbon composites were oriented in different directions and embedded in self-made epoxy resin blocks, which were then sliced using a high-speed saw into sections of about 150 microns. For the mouse brain and spinal cord, a xylene-based fixation was used for sample preparation, as it has been shown to greatly highlight fibers. These were then embedded and sliced in the same way as the phantoms.
The samples were measured during an experiment at the synchrotron with masks featuring different parameters. Simultaneously, a laboratory setup for implementing directional beam tracking was designed, including the source, the sample stage, and the X-ray detector, paving the way for additional applications we expect will extend also after the completion of the project.
The project was strictly technical in nature, so we do not expect a direct and immediate impact on social, economic, or industrial activities. However, the project introduced a new methodology, extending the existing X-ray imaging technique to a new application, representing also a great benefit for the researcher as well as for the host institution in terms of transfer of knowledge and opportunities. The project results will demonstrate the feasibility of X-ray directional beam tracking in biological specimens, as well as its implementation into a laboratory setup. This was made possible through the development of specific elements, including a dedicated sample preparation workflow and algorithms. This resulted in a series of experiments producing a large amount of data, which are expected lead to several scientific publications even after the completion of the project.
More generally, the impact of the project will also be related to the new applications that this methodology will enable in the future. Specifically, the imaging of the central nervous system has significant interest within the scientific community, and the same method can also find applications in materials science, such as in the case of carbon-based composites, which are widely used in the aeronautics and aerospace industries, and for which magnetic resonance imaging is not feasible.
Finally, it is worth mentioning that several companies are currently working on mask-based X-ray detection devices. Therefore, industrial interest in directional beam tracking in the near future cannot be excluded.
More generally, the impact of the project will also be related to the new applications that this methodology will enable in the future. Specifically, the imaging of the central nervous system has significant interest within the scientific community, and the same method can also find applications in materials science, such as in the case of carbon-based composites, which are widely used in the aeronautics and aerospace industries, and for which magnetic resonance imaging is not feasible.
Finally, it is worth mentioning that several companies are currently working on mask-based X-ray detection devices. Therefore, industrial interest in directional beam tracking in the near future cannot be excluded.