Incremental low rank noise reduction for robust infrared tracking of body temperature during medical imaging

Thermal imagery for monitoring of body temperature provides a powerful tool to decrease health risks (e.g., burning) for patients during medical imaging (e.g., magnetic resonance imaging). The presented approach discusses an experiment to simulate radiology conditions with infrared imaging along with an automatic thermal monitoring/tracking system. The thermal tracking system uses an incremental low-rank noise reduction applying incremental singular value decomposition (SVD) and applies color based clustering for initialization of the region of interest (ROI) boundary. Then a particle filter tracks the ROI(s) from the entire thermal stream (video sequence). The thermal database contains 15 subjects in two positions (i.e., sitting, and lying) in front of thermal camera. This dataset is created to verify the robustness of our method with respect to motion-artifacts and in presence of additive noise (2–20%—salt and pepper noise). The proposed approach was tested for the infrared images in the dataset and was able to successfully measure and track the ROI continuously (100% detecting and tracking the temperature of participants), and provided considerable robustness against noise (unchanged accuracy even in 20% additive noise), which shows promising performanc

Mucociliary Transit Assessment Using Automatic Tracking in Phase Contrast X-Ray Images of Live Mouse Nasal Airways

Purpose The rate of mucociliary transit (MCT) is an indicator of the hydration and health of the airways for cystic fibrosis (CF). To determine the effectiveness of cystic fibrosis respiratory therapies, we have developed a novel method to noninvasively quantify the local rate and patterns of MCT behaviour in vivo by using synchrotron phase contrast X-ray imaging (PCXI) to visualise the MCT motion of micron-sized spherical particles deposited onto the airway surfaces of live mice. Methods In this study the baseline MCT behaviour was assessed in the nasal airways of CFTR-null and normal mice which were then treated with hypertonic saline (HS) or mannitol. To assess MCT, the particle motion was tracked throughout the synchrotron PCXI sequences using fully-automated custom image analysis software. Results There was no significant difference in the MCT rate between normal and CFTR-null mice, but the analysis of MCT particle tracking showed that HS may have a longer duration of action in CFTR-null mice than in the normal mice. Conclusion This study demonstrated that changes in MCT rate in CF and normal mouse nasal airways can be measured using PCXI and customised tracking software and used for assessing the effects of airway rehydrating pharmaceutical treatments.Hye-Won Jung, Ivan Lee, Sang, Heon Lee, Kaye Morgan, David Parsons, Martin Donnelle

Making microscopy count: quantitative light microscopy of dynamic processes in living plants

First published: April 2016This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Cell theory has officially reached 350 years of age as the first use of the word ‘cell’ in a biological context can be traced to a description of plant material by Robert Hooke in his historic publication “Micrographia: or some physiological definitions of minute bodies”. The 2015 Royal Microscopical Society Botanical Microscopy meeting was a celebration of the streams of investigation initiated by Hooke to understand at the sub-cellular scale how plant cell function and form arises. Much of the work presented, and Honorary Fellowships awarded, reflected the advanced application of bioimaging informatics to extract quantitative data from micrographs that reveal dynamic molecular processes driving cell growth and physiology. The field has progressed from collecting many pixels in multiple modes to associating these measurements with objects or features that are meaningful biologically. The additional complexity involves object identification that draws on a different type of expertise from computer science and statistics that is often impenetrable to biologists. There are many useful tools and approaches being developed, but we now need more inter-disciplinary exchange to use them effectively. In this review we show how this quiet revolution has provided tools available to any personal computer user. We also discuss the oft-neglected issue of quantifying algorithm robustness and the exciting possibilities offered through the integration of physiological information generated by biosensors with object detection and tracking

Piecewise-stationary motion modeling and iterative smoothing to track heterogeneous particle motions in dense environments

International audienceOne of the major challenges in multiple particle tracking is the capture of extremely heterogeneous movements of objects in crowded scenes. The presence of numerous assignment candidates in the expected range of particle motion makes the tracking ambiguous and induces false positives. Lowering the ambiguity by reducing the search range, on the other hand, is not an option, as this would increase the rate of false negatives. We propose here a piecewise-stationary motion model (PMM) for the particle transport along an iterative smoother that exploits recursive tracking in multiple rounds in forward and backward temporal directions. By fusing past and future information, our method, termed PMMS, can recover fast transitions from freely or confined diffusive to directed motions with linear time complexity. To avoid false positives we complemented recursive tracking with a robust inline estimator of the search radius for assignment (a.k.a. gating), where past and future information are exploited using only two frames at each optimization step. We demonstrate the improvement of our technique on simulated data – especially the impact of density, variation in frame to frame displacements, and motion switching probability. We evaluated our technique on the 2D particle tracking challenge dataset published by Chenouard et al in 2014. Using high SNR to focus on motion modeling challenges, we show superior performance at high particle density. On biological applications, our algorithm allows us to quantify the extremely small percentage of motor-driven movements of fluorescent particles along microtubules in a dense field of unbound, diffusing particles. We also show with virus imaging that our algorithm can cope with a strong reduction in recording frame rate while keeping the same performance relative to methods relying on fast sampling

Quantitative comparison of multiframe data association techniques for particle tracking in time-lapse fluorescence microscopy

Biological studies of intracellular dynamic processes commonly require motion analysis of large numbers of particles in live-cell time-lapse fluorescence microscopy imaging data. Many particle tracking methods have been developed in the past years as a first step toward fully automating this task and enabling high-throughput data processing. Two crucial aspects of any particle tracking method are the detection of relevant particles in the image frames and their linking or association from frame to frame to reconstruct the trajectories. The performance of detection techniques as well as specific combinations of detection and linking techniques for particle tracking have been extensively evaluated in recent studies. Comprehensive evaluations of linking techniques per se, on the other hand, are lacking in the literature. Here we present the results of a quantitative comparison of data association techniques for solving the linking problem in biological particle tracking applications. Nine multiframe and two more traditional two-frame techniques are evaluated as a function of the level of missing and spurious detections in various scenarios. The results indicate that linking techniques are generally more negatively affected by missing detections than by spurious detections. If misdetections can be avoided, there appears to be no need to use sophisticated multiframe linking techniques. However, in the practically likely case of imperfect detections, the latter are a safer choice. Our study provides users and developers with novel information to select the right linking technique for their applications, given a detection technique of known quality. (C) 2015 Elsevier B.V. All rights reserved

Automatic approach for spot detection in microscopy imaging based on image processing and statistical analysis

Abstract: In biological research, fluorescence microscopy has become one of the vital tools used for observation, allowing researchers to study, visualise and image the details of intracel-lular structures which result in better understanding of biology. However, analysis of large numbers of samples is often required to draw statistically verifiable conclusions. Automated methods for analysis of microscopy image data make it possible to handle large datasets, and at the same time reduce the risk of bias imposed by manual techniques in the image analysis pipeline. This work covers automated methods for extracting quan-titative measurements from microscopy images, enabling the detection of spots resulting from different experimental conditions. The work resulted in four main significant con-tributions developed around the microscopy image analysis pipeline. Firstly, an investiga-tion into the importance of spot detection within the automated image analysis pipeline is conducted. Experimental findings show that poor spot detection adversely affected the remainder of the processing pipeline...D.Ing. (Electrical and Electronic Engineering

Kinesin-4 Motor Teams Effectively Navigate Dendritic Microtubule Arrays Via Track Switching And Regulation Of Microtubule Dynamics

The organization of structurally polarized microtubules into networks is critical for efficient cargo transport mediated by the molecular motors dynein and kinesin. The motility properties of molecular motors are best understood in simplified reconstituted systems using single microtubule filaments, as well as in cells with radial microtubule arrangements and axonal compartments with uniformly oriented microtubule arrays. However, it is not understood how active transport occurs in environments with more complicated cytoskeletal geometries, such as the mixed polarity microtubule arrays found in the dendrites of neurons. Here we focus on the plus-end directed kinesin-4 KIF21B motor that is associated with retrograde biased cargo movement in dendrites, despite the mixed polarity microtubule organization. How KIF21B achieves this net directional bias, as well as whether KIF21B is primarily responsible for retrograde directed motility is not known. To understand this, we examined KIF21B motility on mixed polarity microtubule arrays within in vitro systems of increasing complexity and in live neurons. In reconstituted systems with recombinant KIF21B and engineered dynamic antiparallel microtubule bundles or extracted mixed polarity dendritic microtubule arrays, the nucleotide-independent microtubule binding regions of KIF21B were shown to modulate microtubule dynamics and promote directional track switching. For analysis of KIF21B motility, existing methods to automate motor tracking were not ideal, and we developed a segmentation tool called Cega, to detect purified fluorescently labeled kinesin motors moving within a system with high background noise. Interestingly, KIF21B motors did not display the net directional bias along stabilized extracted dendritic microtubule arrays, as seen by KIF21B in live cells. This in combination with the dramatic stabilization of microtubule dynamics by KIF21B suggested that directional bias required microtubule remodeling by KIF21B motors, and thus would only be observed along native dynamic microtubule arrays. Unsurprisingly, KIF21B optogenetic recruitment to dendritic cargo induced net retrograde movement, and both native microtubule dynamics and the secondary microtubule binding regions of KIF21B were required to achieve this directional bias. These results suggest a mechanism where teams of cargo bound KIF21B motors coordinate nucleotide-sensitive and insensitive microtubule binding sites to regulate microtubule stability and promote track switching and ultimately achieve net retrograde movement along the mixed polarity microtubule arrays of dendrites