Freqformer: Frequency-Domain Transformer for 3-D Visualization and Quantification of Human Retinal Circulation

We introduce Freqformer, a novel Transformer-based architecture designed for 3-D, high-definition visualization of human retinal circulation from a single scan in commercial optical coherence tomography angiography (OCTA). Freqformer addresses the challenge of limited signal-to-noise ratio in OCTA volume by utilizing a complex-valued frequency-domain module (CFDM) and a simplified multi-head attention (Sim-MHA) mechanism. Using merged volumes as ground truth, Freqformer enables accurate reconstruction of retinal vasculature across the depth planes, allowing for 3-D quantification of capillary segments (count, density, and length). Our method outperforms state-of-the-art convolutional neural networks (CNNs) and several Transformer-based models, with superior performance in peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM), and learned perceptual image patch similarity (LPIPS). Furthermore, Freqformer demonstrates excellent generalizability across lower scanning density, effectively enhancing OCTA scans with larger fields of view (from 3$\times$3 $mm^{2}$ to 6$\times$6 $mm^{2}$ and 12$\times$12 $mm^{2}$). These results suggest that Freqformer can significantly improve the understanding and characterization of retinal circulation, offering potential clinical applications in diagnosing and managing retinal vascular diseases.

BreakNet: Discontinuity-Resilient Multi-Scale Transformer Segmentation of Retinal Layers

Visible light optical coherence tomography (vis-OCT) is gaining traction for retinal imaging due to its high resolution and functional capabilities. However, the significant absorption of hemoglobin in the visible light range leads to pronounced shadow artifacts from retinal blood vessels, posing challenges for accurate layer segmentation. In this study, we present BreakNet, a multi-scale Transformer-based segmentation model designed to address boundary discontinuities caused by these shadow artifacts. BreakNet utilizes hierarchical Transformer and convolutional blocks to extract multi-scale global and local feature maps, capturing essential contextual, textural, and edge characteristics. The model incorporates decoder blocks that expand pathwaproys to enhance the extraction of fine details and semantic information, ensuring precise segmentation. Evaluated on rodent retinal images acquired with prototype vis-OCT, BreakNet demonstrated superior performance over state-of-the-art segmentation models, such as TCCT-BP and U-Net, even when faced with limited-quality ground truth data. Our findings indicate that BreakNet has the potential to significantly improve retinal quantification and analysis.

Fully Automated OCT-based Tissue Screening System

This study introduces a groundbreaking optical coherence tomography (OCT) imaging system dedicated for high-throughput screening applications using ex vivo tissue culture. Leveraging OCT's non-invasive, high-resolution capabilities, the system is equipped with a custom-designed motorized platform and tissue detection ability for automated, successive imaging across samples. Transformer-based deep learning segmentation algorithms further ensure robust, consistent, and efficient readouts meeting the standards for screening assays. Validated using retinal explant cultures from a mouse model of retinal degeneration, the system provides robust, rapid, reliable, unbiased, and comprehensive readouts of tissue response to treatments. This fully automated OCT-based system marks a significant advancement in tissue screening, promising to transform drug discovery, as well as other relevant research fields.

Monte Carlo Techniques for Addressing Large Errors and Missing Data in Simulation-based Inference

Upcoming astronomical surveys will observe billions of galaxies across cosmic time, providing a unique opportunity to map the many pathways of galaxy assembly to an incredibly high resolution. However, the huge amount of data also poses an immediate computational challenge: current tools for inferring parameters from the light of galaxies take $\gtrsim 10$ hours per fit. This is prohibitively expensive. Simulation-based Inference (SBI) is a promising solution. However, it requires simulated data with identical characteristics to the observed data, whereas real astronomical surveys are often highly heterogeneous, with missing observations and variable uncertainties determined by sky and telescope conditions. Here we present a Monte Carlo technique for treating out-of-distribution measurement errors and missing data using standard SBI tools. We show that out-of-distribution measurement errors can be approximated by using standard SBI evaluations, and that missing data can be marginalized over using SBI evaluations over nearby data realizations in the training set. While these techniques slow the inference process from $\sim 1$ sec to $\sim 1.5$ min per object, this is still significantly faster than standard approaches while also dramatically expanding the applicability of SBI. This expanded regime has broad implications for future applications to astronomical surveys.