smBEVO: A computer vision approach to rapid baseline correction of single-molecule time series

Single-molecule time series inform on the dynamics of molecular mechanisms that are occluded in ensemble-averaged measures. Amplitude-based methods and hidden Markov models (HMMs) frequently used for interpreting these time series require removal of low frequency drift that can be difficult to completely avoid in real world experiments. Current approaches for drift correction primarily involve either tedious manual assignment of the baseline or unsupervised frameworks such as infinite HMMs coupled with baseline nodes that are computationally expensive and unreliable. Here, we develop an image-based method for baseline correction using techniques from computer vision such as lane detection and active contours. The approach is remarkably accurate and efficient, allowing for rapid analysis of single-molecule time series contaminated with nearly any type of slow baseline drift.

Automatic Blob Detection for Dental Caries

Dental Caries are one of the most prevalent chronic diseases around the globe. Detecting carious lesions is a challenging task. Conventional computer aided diagnosis and detection methods in the past have heavily relied on the visual inspection of teeth. These methods are only effective on large and clearly visible caries on affected teeth. Conventional methods have been limited in performance due to the complex visual characteristics of dental caries images, which consist of hidden or inaccessible lesions. The early detection of dental caries is an important determinant for treatment and benefits much from the introduction of new tools, such as dental radiography. In this paper, we propose a deep learning-based technique for dental caries detection namely: blob detection. The proposed technique automatically detects hidden and inaccessible dental caries lesions in bitewing radio-graphs. The approach employs data augmentation to increase the number of images in the data set to have a total of 11,114 dental images. Image pre-processing on the data set was through the use of Gaussian blur filters. Image segmentation was handled through thresholding, erosion and dilation morphology, while image boundary detection was achieved through active contours method. Furthermore, the deep learning based network through the sequential model in Keras extracts features from the images through blob detection. Finally, a convexity threshold value of 0.9 is introduced to aid in the classification of caries as either present or not present. The process of detection and classifying dental caries achieved the results of 97% and 96% for the precision and recall values, respectively.

Automated left atrial time-resolved segmentation in MRI long-axis cine images using active contours

Background Segmentation of the left atrium (LA) is required to evaluate atrial size and function, which are important imaging biomarkers for a wide range of cardiovascular conditions, such as atrial fibrillation, stroke, and diastolic dysfunction. LA segmentations are currently being performed manually, which is time-consuming and observer-dependent. Methods This study presents an automated image processing algorithm for time-resolved LA segmentation in cardiac magnetic resonance imaging (MRI) long-axis cine images of the 2-chamber (2ch) and 4-chamber (4ch) views using active contours. The proposed algorithm combines mitral valve tracking, automated threshold calculation, edge detection on a radially resampled image, edge tracking based on Dijkstra’s algorithm, and post-processing involving smoothing and interpolation. The algorithm was evaluated in 37 patients diagnosed mainly with paroxysmal atrial fibrillation. Segmentation accuracy was assessed using the Dice similarity coefficient (DSC) and Hausdorff distance (HD), with manual segmentations in all time frames as the reference standard. For inter-observer variability analysis, a second observer performed manual segmentations at end-diastole and end-systole on all subjects. Results The proposed automated method achieved high performance in segmenting the LA in long-axis cine sequences, with a DSC of 0.96 for 2ch and 0.95 for 4ch, and an HD of 5.5 mm for 2ch and 6.4 mm for 4ch. The manual inter-observer variability analysis had an average DSC of 0.95 and an average HD of 4.9 mm. Conclusion The proposed automated method achieved performance on par with human experts analyzing MRI images for evaluation of atrial size and function.