VolPy: Automated and scalable analysis pipelines for voltage imaging datasets.

Voltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (>800MB/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present VolPy, an automated and scalable pipeline to pre-process voltage imaging datasets. VolPy features motion correction, memory mapping, automated segmentation, denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation, we introduce a corpus of 24 manually annotated datasets from different preparations, brain areas and voltage indicators. We benchmark VolPy against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that VolPy's performance in spike extraction and scalability are state-of-the-art.

ConIQA: A deep learning method for perceptual image quality assessment with limited data.

Effectively assessing the realism and naturalness of images in virtual (VR) and augmented (AR) reality applications requires Full Reference Image Quality Assessment (FR-IQA) metrics that closely align with human perception. Deep learning-based IQAs that are trained on human-labeled data have recently shown promise in generic computer vision tasks. However, their performance decreases in applications where perfect matches between the reference and the distorted images should not be expected, or whenever distortion patterns are restricted to specific domains. Tackling this issue necessitates training a task-specific neural network, yet generating human-labeled FR-IQAs is costly, and deep learning typically demands substantial labeled data. To address these challenges, we developed ConIQA, a deep learning-based IQA that leverages consistency training and a novel data augmentation method to learn from both labeled and unlabeled data. This makes ConIQA well-suited for contexts with scarce labeled data. To validate ConIQA, we considered the example application of Computer-Generated Holography (CGH) where specific artifacts such as ringing, speckle, and quantization errors routinely occur, yet are not explicitly accounted for by existing IQAs. We developed a new dataset, HQA1k, that comprises 1000 natural images each paired with an image rendered using various popular CGH algorithms, and quality-rated by thirteen human participants. Our results show that ConIQA achieves superior Pearson (0.98), Spearman (0.965), and Kendall's tau (0.86) correlations over fifteen FR-IQA metrics by up to 5%, showcasing significant improvements in aligning with human perception on the HQA1k dataset.

Advances in computer-generated holography for targeted neuronal modulation.

Genetically encoded calcium indicators and optogenetics have revolutionized neuroscience by enabling the detection and modulation of neural activity with single-cell precision using light. To fully leverage the immense potential of these techniques, advanced optical instruments that can place a light on custom ensembles of neurons with a high level of spatial and temporal precision are required. Modern light sculpting techniques that have the capacity to shape a beam of light are preferred because they can precisely target multiple neurons simultaneously and modulate the activity of large ensembles of individual neurons at rates that match natural neuronal dynamics. The most versatile approach, computer-generated holography (CGH), relies on a computer-controlled light modulator placed in the path of a coherent laser beam to synthesize custom three-dimensional (3D) illumination patterns and illuminate neural ensembles on demand. Here, we review recent progress in the development and implementation of fast and spatiotemporally precise CGH techniques that sculpt light in 3D to optically interrogate neural circuit functions.

Cluster-based filtering framework for speckle reduction in OCT images.

Optical coherence tomography (OCT) has become a popular modality in the dermatology discipline due to its moderate resolution and penetration depth. OCT images, however, contain a grainy pattern called speckle. To date, a variety of filtering techniques have been introduced to reduce speckle in OCT images. However, further improvement is required to reduce edge smoothing and the deterioration of small structures in OCT images after despeckling. In this manuscript, we present a novel cluster-based speckle reduction framework (CSRF) that consists of a clustering method, followed by a despeckling method. Since edges are borders of two adjacent clusters, the proposed framework leaves the edges intact. Moreover, the multiplicative speckle noise could be modeled as additive noise in each cluster. To evaluate the performance of CSRF and demonstrate its generic nature, a clustering method, namely k-means (KM), and, two pixelwise despeckling algorithms, including Lee filter (LF) and adaptive Wiener filter (AWF), are used. The results indicate that CSRF significantly improves the performance of despeckling algorithms. These improvements are evaluated on healthy human skin images in vivo using two numerical assessment measures including signal-to-noise ratio (SNR), and structural similarity index (SSIM).