MOTIVATION: Biological studies of dynamic processes in living cells often require accurate particle tracking as a first step toward quantitative analysis. Although many particle tracking methods have been developed for this purpose, they are typically based on prior assumptions about the particle dynamics, and/or they involve careful tuning of various algorithm parameters by the user for each application. This may make existing methods difficult to apply by non-expert users and to a broader range of tracking problems. Recent advances in deep-learning techniques hold great promise in eliminating these disadvantages, as they can learn how to optimally track particles from example data. RESULTS: Here, we present a deep-learning-based method for the data association stage of particle tracking. The proposed method uses convolutional neural networks and long short-term memory networks to extract relevant dynamics features and predict the motion of a particle and the cost of linking detected particles from one time point to the next. Comprehensive evaluations on datasets from the particle tracking challenge demonstrate the competitiveness of the proposed deep-learning method compared to the state of the art. Additional tests on real-time-lapse fluorescence microscopy images of various types of intracellular particles show the method performs comparably with human experts. AVAILABILITY AND IMPLEMENTATION: The software code implementing the proposed method as well as a description of how to obtain the test data used in the presented experiments will be available for non-commercial purposes from https://github.com/yoyohoho0221/pt_linking. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Percutaneous coronary intervention (PCI) is typically performed with image guidance using X-ray angiograms in which coronary arteries are opacified with X-ray opaque contrast agents. Interventional cardiologists typically navigate instruments using non-contrast-enhanced fluoroscopic images, since higher use of contrast agents increases the risk of kidney failure. When using fluoroscopic images, the interventional cardiologist needs to rely on a mental anatomical reconstruction. This paper reports on the development of a novel dynamic coronary roadmapping approach for improving visual feedback and reducing contrast use during PCI. The approach compensates cardiac and respiratory induced vessel motion by ECG alignment and catheter tip tracking in X-ray fluoroscopy, respectively. In particular, for accurate and robust tracking of the catheter tip, we proposed a new deep learning based Bayesian filtering method that integrates the detection outcome of a convolutional neural network and the motion estimation between frames using a particle filtering framework. The proposed roadmapping and tracking approaches were validated on clinical X-ray images, achieving accurate performance on both catheter tip tracking and dynamic coronary roadmapping experiments. In addition, our approach runs in real-time on a computer with a single GPU and has the potential to be integrated into the clinical workflow of PCI procedures, providing cardiologists with visual guidance during interventions without the need of extra use of contrast agent.

Up-to-date 3D building models are important for many applications. Airborne very high resolution (VHR) images often acquired annually give an opportunity to create an up-to-date 3D model. Building segmentation is often the first and utmost step. Convolutional neural networks (CNNs) draw lots of attention in interpreting VHR images as they can learn very effective features for very complex scenes. This paper employs Mask R-CNN to address two problems in building segmentation: detecting different scales of building and segmenting buildings to have accurately segmented edges. Mask R-CNN starts from feature pyramid network (FPN) to create different scales of semantically rich features. FPN is integrated with region proposal network (RPN) to generate objects with various scales with the corresponding optimal scale of features. The features with high and low levels of information are further used for better object classification of small objects and for mask prediction of edges. The method is tested on ISPRS benchmark dataset by comparing results with the fully convolutional networks (FCN), which merge high and low level features by a skip-layer to create a single feature for semantic segmentation. The results show that Mask R-CNN outperforms FCN with around 15% in detecting objects, especially in detecting small objects. Moreover, Mask R-CNN has much better results in edge region than FCN. The results also show that choosing the range of anchor scales in Mask R-CNN is a critical factor in segmenting different scale of objects. This paper provides an insight into how a good anchor scale for different dataset should be chosen.

Quantitative analysis of dynamic processes in living cells using time-lapse microscopy requires not only accurate tracking of every particle in the images, but also reliable extraction of biologically relevant parameters from the resulting trajectories. Whereas many methods exist to perform the tracking task, there is still a lack of robust solutions for subsequent parameter extraction and analysis. Here a novel method is presented to address this need. It uses for the first time a deep learning approach to segment single particle trajectories into consistent tracklets (trajectory segments that exhibit one type of motion) and then performs moment scaling spectrum analysis of the tracklets to estimate the number of mobility classes and their associated parameters, providing rich fundamental knowledge about the behavior of the particles under study. Experiments on in-house datasets as well as publicly available particle tracking data for a wide range of proteins with different dynamic behavior demonstrate the broad applicability of the method.

Diagnosis of patients suffering from small-fiber neuropathy is a challenging task and requires accurate measurement of the density of nerve fibers crossing the dermal-epidermal junction in the skin. Currently this is typically done by expert manual counting in microscopy images of sliced and stained skin biopsies. It is a rather subjective and labor-intensive process that would benefit greatly from more automated approaches. Previously we have explored classical image processing methods for this, with very limited success. Here we explore the potential of convolutional neural networks and deep learning for the task. The results of preliminary experiments show the networks perform close to the expert and outperform novices and our previous method.