Biology subjects

DiGiacomo, P.

Publications and source records attributed to DiGiacomo, P..

3 recordsLinked to original sources

bioRxiv2025

Denoising 7T Structural MRI with Conditional Generative Diffusion Models

Purpose7T MRI offers ultra-high resolution and improved sensitivity for iron deposition in neurodegenerative disorders, but commonly used acquisitions are long and hence challenging, especially for elderly subjects. Efficiently denoising a short acquisition to achieve the image quality of a longer acquisition would be of translational benefit. Materials and MethodsWe introduce a conditional diffusion model derived from generative AI (a 7T Conditional Diffusion Model, 7TCDM) that was trained on native single-acquisition 2D reconstructions and referenced multi-repetition images to guide the denoising process and improve SNR and contrast. 7TCDM model was tested on 2D T2-weighted gradient-echo imaging from 19 participants, including healthy controls and individuals with mild cognitive impairment or Alzheimers disease (AD). 7TCDMs performance was assessed using Mean Squared Error (MSE), Peak Signal-to-Noise Ratio (PSNR), Structural Similarity Index Measure (SSIM), and comprehensive reader studies. ResultsReferencing the multi-repetition ground truth, 7TCDM improved the single-acquisition original image by 29.1% in MSE, 5.8% in PSNR, and 9.4% in SSIM, and outperformed convolutional neural network-based models in all metrics. Expert rater evaluations confirmed superior image quality, with significantly enhanced detail and contrast preservation in regions such as the hippocampi, white matter lesions, and small cortical veins. The model also demonstrated robust performance in both the concurrently acquired and publicly available 3D multi-echo gradient echo acquisitions, which the model was not trained on. ConclusionsThe 7T Conditional Diffusion Model provides high-quality denoised images from shorter scans, increasing the feasibility of scanning patients in shorter times while preserving essential anatomical and pathological details.

neuroscience↗

bioRxiv2025

Precise MRI-Histology Coregistration of Paraffin-Embedded Tissue with Blockface Imaging

Magnetic resonance imaging (MRI) provides 3D spatial information on tissue, yet it lacks at the molecular level. In contrast, histology provides cellular and molecular information, but it lacks the 3D spatial context and direct in vivo translation. Coregistering the two is key for the 3D-embedding of histological details, validating pathological MRI findings, and finding quantitative imaging biomarkers of neurodegenerative diseases. However, coregistration is challenging due to non-linear distortions of the tissue from histological processing and sectioning leading to microscopic and macroscopic nonlinear 3D deformations between specimen MRI and stained histology sections. To address this, we developed a novel pipeline, named Brewsters Blockface Quantification (BBQ), integrating robust optical approaches with innovative 2D and 3D registration algorithms to achieve precise volumetric alignment of specimen MRI data with histological images. On a variety of brain tissue specimens from distinct anatomical regions and across multiple species, our methodology generated blockface volumes with minimal distortion and artifacts. Using these blockface volumes as an intermediary, we achieve a precise alignment between MRI and histology slides, yielding registration results with an overlapping Dice score of [~]90% for whole tissue alignment between MRI and blockface volumes, and >95% for 2D MRI-histology registration. This correlative MRI-histology pipeline with robust 2D and 3D coregistration methods promises to enhance our understanding of neurodegenerative diseases and aid the development of MRI-based disease biomarkers.

bioengineering↗

bioRxiv2022

Microstructural alterations in tract development in college football: a longitudinal diffusion MRI study

Background and ObjectivesRepeated concussive and sub-concussive impacts in high-contact sports can affect the brains microstructure, which can be studied using diffusion MRI. Most prior imaging studies, however, employ a cross-sectional design, do not include low-contact players as controls, or use traditional diffusion tensor imaging without investigating novel tractspecific microstructural metrics. MethodsWe examined brain microstructure in 63 high-contact (American football) and 34 low-contact (volleyball) collegiate athletes with up to 4 years of follow-up (315 total scans) using advanced diffusion MRI, a comprehensive set of multi-compartment models, and automated fiber quantification tools. We investigated diffusion metrics along the length of tracts using nested linear mixed-effects models to ascertain the acute and chronic effects of sub-concussive and concussive impacts, as well as associations between diffusion changes with clinical, behavioral, and sports-related measures. ResultsSignificant longitudinal increases in fractional anisotropy and axonal water fraction were detected in volleyball players, but not in football players, along with decreases in radial and mean diffusivity as well as orientation dispersion index (all findings absolute T-statistic > 3.5, p < .0001). This pattern was present in the callosum forceps minor, left superior longitudinal fasciculus, left thalamic radiation, and right cingulum hippocampus. Longitudinal group differences were more prominent and observed in a larger number of tracts in concussed (previously or in-study) football players (p < .0001), while smaller effects were noted in un-concussed players. An analysis of immediate-post concussion scans in football players demonstrated a transient localized increase in axial diffusivity, mean and radial kurtosis in the left uncinate and right cingulum hippocampus (p < .0001). Finally, football players with high position-based sub-concussive risk demonstrated increased orientation dispersion index over time (p < .0001). DiscussionThe observed longitudinal changes in our volleyball cohort likely reflect normal development in this age range, while the relative attenuation of these effects seen in football, and especially concussed athletes, could possibly reveal diminished myelination, altered axonal calibers, or depressed pruning processes leading to a static, non-decreasing axonal dispersion. This prospective longitudinal study demonstrates significantly divergent tract-specific trajectories of brain microstructure, possibly reflecting a concussive and/or repeated sub-concussive impact-related alteration of normal white matter development in football athletes.

neuroscience↗