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Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images.

Automated detection of specific cells in three-dimensional datasets such as whole-brain light-sheet image stacks is challenging. Here, we present DELiVR, a virtual reality-trained deep-learning pipeline for detecting c-Fos+cells as markers for neuronal activity in cleared mouse brains. Virtual reality annotation substantially accelerated training data generation, enabling DELiVR to outperform state-of-the-art cell-segmenting approaches. Our pipeline is available in a user-friendly Docker container that runs with a standalone Fiji plugin. DELiVR features a comprehensive toolkit for data visualization and can be customized to other cell types of interest, as we did here for microglia somata, using Fiji for dataset-specific training. We applied DELiVR to investigate cancer-related brain activity, unveiling an activation pattern that distinguishes weight-stable cancer from cancers associated with weight loss. Overall, DELiVR is a robust deep-learning tool that does not require advanced coding skills to analyze whole-brain imaging data in health and disease.

Layered, two-dimensional (2D) materials are promising for next-generation photonics devices. Typically, the thickness of mechanically cleaved flakes and chemical vapor deposited thin films is distributed randomly over a large area, where accurate identification of atomic layer numbers is time-consuming. Hyperspectral imaging microscopy yields spectral information that can be used to distinguish the spectral differences of varying thickness specimens. However, its spatial resolution is relatively low due to the spectral imaging nature. In this work, we present a 3D deep learning solution called DALM (deep-learning-enabled atomic layer mapping) to merge hyperspectral reflection images (high spectral resolution) and RGB images (high spatial resolution) for the identification and segmentation of MoS2flakes with mono-, bi-, tri-, and multilayer thicknesses. DALM is trained on a small set of labeled images, automatically predicts layer distributions and segments individual layers with high accuracy, and shows robustness to illumination and contrast variations. Further, we show its advantageous performance over the state-of-the-art model that is solely based on RGB microscope images. This AI-supported technique with high speed, spatial resolution, and accuracy allows for reliable computer-aided identification of atomically thin materials.