Search for: All records

The size of image volumes in connectomics studies now reaches terabyte and often petabyte scales with a great diversity of appearance due to different sample preparation procedures. However, manual annotation of neuronal structures (e.g., synapses) in these huge image volumes is time-consuming, leading to limited labeled training data often smaller than 0.001% of the large-scale image volumes in application. Methods that can utilize in-domain labeled data and generalize to out-of-domain unlabeled data are in urgent need. Although many domain adaptation approaches are proposed to address such issues in the natural image domain, few of them have been evaluated on connectomics data due to a lack of domain adaptation benchmarks. Therefore, to enable developments of domain adaptive synapse detection methods for large-scale connectomics applications, we annotated 14 image volumes from a biologically diverse set of Megaphragma viggianii brain regions originating from three different whole-brain datasets and organized the WASPSYN challenge at ISBI 2023. The annotations include coordinates of pre-synapses and post-synapses in the 3D space, together with their one-to-many connectivity information. This paper describes the dataset, the tasks, the proposed baseline, the evaluation method, and the results of the challenge. Limitations of the challenge and the impact on neuroscience research are also discussed. The challenge is and will continue to be available at https://codalab.lisn.upsaclay.fr/competitions/9169. Successful algorithms that emerge from our challenge may potentially revolutionize real-world connectomics research and further the cause that aims to unravel the complexity of brain structure and function. 

Abstract Natural hazards cause disruptions in access to critical facilities, such as grocery stores, impeding residents’ ability to prepare for and cope with hardships during the disaster and recovery; however, disrupted access to critical facilities is not equal for all residents of a community. In this study, we examine disparate access to grocery stores in the context of the 2017 Hurricane Harvey in Harris County, Texas. We utilized high-resolution location-based datasets in implementing spatial network analysis and dynamic clustering techniques to uncover the overall disparate access to grocery stores for socially vulnerable populations during different phases of the disaster. Three access indicators are examined using network-centric measures: number of unique stores visited, average trip time to stores, and average distance to stores. These access indicators help us capture three dimensions of access: redundancy , rapidity , and proximity . The findings show the insufficiency of focusing merely on the distributional factors, such as location in a food desert and number of facilities, to capture the disparities in access, especially during the preparation and impact/short-term recovery periods. Furthermore, the characterization of access by considering combinations of access indicators reveals that flooding disproportionally affects socially vulnerable populations. High-income areas have better access during the preparation period as they are able to visit a greater number of stores and commute farther distances to obtain supplies. The conclusions of this study have important implications for urban development (facility distribution), emergency management, and resource allocation by identifying areas most vulnerable to disproportionate access impacts using more equity-focused and data-driven approaches. 

Abstract The objective of this study was to investigate the importance of multiple county-level features in the trajectory of COVID-19. We examined feature importance across 2787 counties in the United States using data-driven machine learning models. Existing mathematical models of disease spread usually focused on the case prediction with different infection rates without incorporating multiple heterogeneous features that could impact the spatial and temporal trajectory of COVID-19. Recognizing this, we trained a data-driven model using 23 features representing six key influencing factors affecting the pandemic spread: social demographics of counties, population activities, mobility within the counties, movement across counties, disease attributes, and social network structure. Also, we categorized counties into multiple groups according to their population densities, and we divided the trajectory of COVID-19 into three stages: the outbreak stage, the social distancing stage, and the reopening stage. The study aimed to answer two research questions: (1) The extent to which the importance of heterogeneous features evolved at different stages; (2) The extent to which the importance of heterogeneous features varied across counties with different characteristics. We fitted a set of random forest models to determine weekly feature importance. The results showed that: (1) Social demographic features, such as gross domestic product, population density, and minority status maintained high-importance features throughout stages of COVID-19 across 2787 studied counties; (2) Within-county mobility features had the highest importance in counties with higher population densities; (3) The feature reflecting the social network structure (Facebook, social connectedness index), had higher importance for counties with higher population densities. The results showed that the data-driven machine learning models could provide important insights to inform policymakers regarding feature importance for counties with various population densities and at different stages of a pandemic life cycle.