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Free, publicly-accessible full text available July 9, 2024
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Abstract Motivation Morphological analyses with flatmount fluorescent images are essential to retinal pigment epithelial (RPE) aging studies and thus require accurate RPE cell segmentation. Although rapid technology advances in deep learning semantic segmentation have achieved great success in many biomedical research, the performance of these supervised learning methods for RPE cell segmentation is still limited by inadequate training data with high-quality annotations.
Results To address this problem, we develop a Self-Supervised Semantic Segmentation (S4) method that utilizes a self-supervised learning strategy to train a semantic segmentation network with an encoder–decoder architecture. We employ a reconstruction and a pairwise representation loss to make the encoder extract structural information, while we create a morphology loss to produce the segmentation map. In addition, we develop a novel image augmentation algorithm (AugCut) to produce multiple views for self-supervised learning and enhance the network training performance. To validate the efficacy of our method, we applied our developed S4 method for RPE cell segmentation to a large set of flatmount fluorescent microscopy images, we compare our developed method for RPE cell segmentation with other state-of-the-art deep learning approaches. Compared with other state-of-the-art deep learning approaches, our method demonstrates better performance in both qualitative and quantitative evaluations, suggesting its promising potential to support large-scale cell morphological analyses in RPE aging investigations.
Availability and implementation The codes and the documentation are available at: https://github.com/jkonglab/S4_RPE.
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Abstract Advances in microfluidic technologies rely on engineered 3D flow patterns to manipulate samples at the microscale. However, current methods for mapping flows only provide limited 3D and temporal resolutions or require highly specialized optical set-ups. Here, we present a simple defocusing approach based on brightfield microscopy and open-source software to map micro-flows in 3D at high spatial and temporal resolution. Our workflow is both integrated in ImageJ and modular. We track seed particles in 2D before classifying their Z-position using a reference library. We compare the performance of a traditional cross-correlation method and a deep learning model in performing the classification step. We validate our method on three highly relevant microfluidic examples: a channel step expansion and displacement structures as single-phase flow examples, and droplet microfluidics as a two-phase flow example. First, we elucidate how displacement structures efficiently shift large particles across streamlines. Second, we reveal novel recirculation structures and folding patterns in the internal flow of microfluidic droplets. Our simple and widely accessible brightfield technique generates high-resolution flow maps and it will address the increasing demand for controlling fluids at the microscale by supporting the efficient design of novel microfluidic structures.
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Abstract Motivation Predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) patients accurately is direly needed for clinical decision making. pCR is also regarded as a strong predictor of overall survival. In this work, we propose a deep learning system to predict pCR to NAC based on serial pathology images stained with hematoxylin and eosin and two immunohistochemical biomarkers (Ki67 and PHH3). To support human prior domain knowledge-based guidance and enhance interpretability of the deep learning system, we introduce a human knowledge-derived spatial attention mechanism to inform deep learning models of informative tissue areas of interest. For each patient, three serial breast tumor tissue sections from biopsy blocks were sectioned, stained in three different stains and integrated. The resulting comprehensive attention information from the image triplets is used to guide our prediction system for prognostic tissue regions.
Results The experimental dataset consists of 26 419 pathology image patches of 1000×1000 pixels from 73 TNBC patients treated with NAC. Image patches from randomly selected 43 patients are used as a training dataset and images patches from the rest 30 are used as a testing dataset. By the maximum voting from patch-level results, our proposed model achieves a 93% patient-level accuracy, outperforming baselines and other state-of-the-art systems, suggesting its high potential for clinical decision making.
Availability and implementation The codes, the documentation and example data are available on an open source at: https://github.com/jkonglab/PCR_Prediction_Serial_WSIs_biomarkers
Supplementary information Supplementary data are available at Bioinformatics online.
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The coronavirus disease 2019 (COVID-19) epidemic poses a threat to the everyday life of people worldwide and brings challenges to the global health system. During this outbreak, it is critical to find creative ways to extend the reach of informatics into every person in society. Although there are many websites and mobile applications for this purpose, they are insufficient in reaching vulnerable populations like older adults who are not familiar with using new technologies to access information. In this paper, we propose an AI-enabled chatbot assistant that delivers real-time, useful, context-aware, and personalized information about COVID-19 to users, especially older adults. To use the assistant, a user simply speaks to it through a mobile phone or a smart speaker. This natural and interactive interface does not require the user to have any technical background. The virtual assistant was evaluated in the lab environment through various types of use cases. Preliminary qualitative test results demonstrate a reasonable precision and recall rate.more » « less
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The use of mobile devices, especially smartphones, has become popular in recent years. There is an increasing need for cross-device interaction techniques that seamlessly integrate mobile devices and large display devices together. This paper develops a novel cross-device cursor position system that maps a mobile device’s movement on a flat surface to a cursor’s movement on a large display. The system allows a user to directly manipulate objects on a large display device through a mobile device and supports seamless cross-device data sharing without physical distance restrictions. To achieve this, we utilize sound localization to initialize the mobile device position as the starting location of a cursor on the large screen. Then, the mobile device’s movement is detected through an accelerometer and is accordingly translated to the cursor’s movement on the large display using machine learning models. In total, 63 features and 10 classifiers were employed to construct the machine learning models for movement detection. The evaluation results have demonstrated that three classifiers, in particular, gradient boosting, linear discriminant analysis (LDA), and naïve Bayes, are suitable for detecting the movement of a mobile device.more » « less
