Ryan A. Kerekes

Selecting a composite correlation filter design: a survey and comparative study

Many composite correlation filter designs have been proposed for solving a wide variety of target detection and pattern recognition problems. Due to the large number of available designs, however, it is often unclear how to select the best design for a particular application. We present a theoretical survey and an empirical comparison of several popular composite correlation filter designs. Using a database of rotational target imagery, we show that some such filter designs appear to be better choices than others under computational and performance constraints. We compare filter performance in terms of noise tolerance, computational load, generalization ability, and distortion in order to provide a multifaceted examination of the characteristics of various filter designs.

Pose measurement and tracking system for motion-correction of unrestrained small animal PET/SPECT imaging

An optical landmark-based pose measurement and tracking system is under development to provide in-scan animal position data for a new SPECT imaging system for unrestrained laboratory animals. The animal position and orientation data provides motion correction during image reconstruction. This paper describes new developments and progress using landmark markers placed on the animal along with strobed infrared lighting with improvements in accuracy for the extraction of head feature positions during motion. A stereo infrared imaging approach acquires images of the markers through a transparent enclosure, segments the markers, corrects for distortion and rejects unwanted reflections. Software estimates intrinsic as well as extrinsic camera calibration parameters and provides a full six degree-of-freedom (DOF) camera-to-camera calibration. A robust stereo point correspondence and 3D measurement calculation based on the fundamental matrix provides the pose at camera frame rates. Experimental testing has been conducted on calibrated fixtures with six DOF measurement capabilities as well as on live laboratory mice. Results show significantly improved accuracy and repeatability of the measurements. The live mouse results have demonstrated that reliable, accurate tracking measurements can be consistently achieved for the full SPECT image acquisition.

Automated 3-D tracking of centrosomes in sequences of confocal image stacks

In order to facilitate the study of neuron migration, we propose a method for 3-D detection and tracking of centrosomes in time-lapse confocal image stacks of live neuron cells. We combine Laplacian-based blob detection, adaptive thresholding, and the extraction of scale and roundness features to find centrosome-like objects in each frame. We link these detections using the joint probabilistic data association filter (JPDAF) tracking algorithm with a Newtonian state-space model tailored to the motion characteristics of centrosomes in live neurons. We apply our algorithm to image sequences containing multiple cells, some of which had been treated with motion-inhibiting drugs. We provide qualitative results and quantitative comparisons to manual segmentation and tracking results showing that our average motion estimates agree to within 13% of those computed manually by neurobiologists.

Restoring auditory cortex plasticity in adult mice by restricting thalamic adenosine signaling

Reopening a critical period Young brains, compared with adult brains, are plastic. This phenomenon has given rise to the concept of critical periods, during which acquisition of certain skills is optimal. In mice, an auditory critical period is only open in early postnatal days. The youthful brain tunes circuits to sounds in its environment in a way that the adult brain does not. This facility may form the basis for childhood language acquisition in humans. Blundon et al. show that by manipulating adenosine signaling in mice, some plasticity of the adult auditory cortex can be regained (see the Perspective by Kehayas and Holmaat). Disruption of adenosine production or adenosine receptor signaling in adult mice leads to improved tone discrimination abilities. Science, this issue p. 1352; see also p. 1335 The auditory cortex of adult mice acquires juvenile flexibility if adenosine signaling is disrupted. Circuits in the auditory cortex are highly susceptible to acoustic influences during an early postnatal critical period. The auditory cortex selectively expands neural representations of enriched acoustic stimuli, a process important for human language acquisition. Adults lack this plasticity. Here we show in the murine auditory cortex that juvenile plasticity can be reestablished in adulthood if acoustic stimuli are paired with disruption of ecto-5′-nucleotidase–dependent adenosine production or A1–adenosine receptor signaling in the auditory thalamus. This plasticity occurs at the level of cortical maps and individual neurons in the auditory cortex of awake adult mice and is associated with long-term improvement of tone-discrimination abilities. We conclude that, in adult mice, disrupting adenosine signaling in the thalamus rejuvenates plasticity in the auditory cortex and improves auditory perception.

Leading-process actomyosin coordinates organelle positioning and adhesion receptor dynamics in radially migrating cerebellar granule neurons

BackgroundDuring brain development, neurons migrate from germinal zones to their final positions to assemble neural circuits. A unique saltatory cadence involving cyclical organelle movement (e.g., centrosome motility) and leading-process actomyosin enrichment prior to nucleokinesis organizes neuronal migration. While functional evidence suggests that leading-process actomyosin is essential for centrosome motility, the role of the actin-enriched leading process in globally organizing organelle transport or traction forces remains unexplored.ResultsWe show that myosin ii motors and F-actin dynamics are required for Golgi apparatus positioning before nucleokinesis in cerebellar granule neurons (CGNs) migrating along glial fibers. Moreover, we show that primary cilia are motile organelles, localized to the leading-process F-actin-rich domain and immobilized by pharmacological inhibition of myosin ii and F-actin dynamics. Finally, leading process adhesion dynamics are dependent on myosin ii and F-actin.ConclusionsWe propose that actomyosin coordinates the overall polarity of migrating CGNs by controlling asymmetric organelle positioning and cell-cell contacts as these cells move along their glial guides.

Automatic detection, segmentation and characterization of retinal horizontal neurons in large-scale 3D confocal imagery

Automatic analysis of neuronal structure from wide-field-of-view 3D image stacks of retinal neurons is essential for statistically characterizing neuronal abnormalities that may be causally related to neural malfunctions or may be early indicators for a variety of neuropathies. In this paper, we study classification of neuron fields in large-scale 3D confocal image stacks, a challenging neurobiological problem because of the low spatial resolution imagery and presence of intertwined dendrites from different neurons. We present a fully automated, four-step processing approach for neuron classification with respect to the morphological structure of their dendrites. In our approach, we first localize each individual soma in the image by using morphological operators and active contours. By using each soma position as a seed point, we automatically determine an appropriate threshold to segment dendrites of each neuron. We then use skeletonization and network analysis to generate the morphological structures of segmented dendrites, and shape-based features are extracted from network representations of each neuron to characterize the neuron. Based on qualitative results and quantitative comparisons, we show that we are able to automatically compute relevant features that clearly distinguish between normal and abnormal cases for postnatal day 6 (P6) horizontal neurons.

Retinoblastoma (Rb) regulates laminar dendritic arbor reorganization in retinal horizontal neurons

Neuronal differentiation with respect to the acquisition of synaptic competence needs to be regulated precisely during neurogenesis to ensure proper formation of circuits at the right place and time in development. This regulation is particularly important for synaptic triads among photoreceptors, horizontal cells (HCs), and bipolar cells in the retina, because HCs are among the first cell types produced during development, and bipolar cells are among the last. HCs undergo a dramatic transition from vertically oriented neurites that form columnar arbors to overlapping laminar dendritic arbors with differentiation. However, how this process is regulated and coordinated with differentiation of photoreceptors and bipolar cells remains unknown. Previous studies have suggested that the retinoblastoma (Rb) tumor suppressor gene may play a role in horizontal cell differentiation and synaptogenesis. By combining genetic mosaic analysis of individual synaptic triads with neuroanatomic analyses and multiphoton live imaging of developing HCs, we found that Rb plays a cell-autonomous role in the reorganization of horizontal cell neurites as they differentiate. Aberrant vertical processes in Rb-deficient HCs form ectopic synapses with rods in the outer nuclear layer but lack bipolar dendrites. Although previous reports indicate that photoreceptor abnormalities can trigger formation of ectopic synapses, our studies now demonstrate that defects in a postsynaptic partner contribute to the formation of ectopic photoreceptor synapses in the mammalian retina.

Fully automated segmentation and characterization of the dendritic trees of retinal horizontal neurons

We introduce a new fully automated method for segmenting and characterizing the dendritic tree of neurons in confocal image stacks. Our method is aimed at wide-field-of-view, low-resolution imagery of retinal neurons in which dendrites can be intertwined and difficult to follow. The approach is based on 3-D skeletonization and includes a method for automatically determining an appropriate global threshold as well as a soma detection algorithm. We provide the details of the algorithm and a qualitative performance comparison against a commercially available neurite tracing software package, showing that a segmentation produced by our method more closely matches the ground-truth segmentation.

Two methods for tracking small animals in SPECT imaging

High-resolution single photon emission computed tomography (SPECT) and X-ray computed tomography (CT) imaging have proven to be useful techniques for non-invasively monitoring mutations and disease progression in small animals. A need to perform in vivo studies of non-anesthetized animals has led to the development of a small-animal imaging system that integrates SPECT imaging equipment with a pose-tracking system. The pose of the animal is monitored and recorded during the SPECT scan using either laser-generated surfaces or infrared-reflective markers affixed to the animal. The reflective marker method measures motion by stereoscopically imaging an arrangement of illuminated markers. The laser-based method is proposed as a possible alternative to the reflector method with the advantage that it is a non-contact system. A three-step technique is described for calibrating the surface acquisition system so that quantitative surface measurements can be obtained. The acquired surfaces can then be registered to a reference surface using the iterative closest point (ICP) algorithm to determine the relative pose of the live animal and correct for any movement during the scan. High accuracy measurement results have been obtained from both methods.

Automated Tracing of Horizontal Neuron Processes During Retinal Development

In the developing mammalian retina, horizontal neurons undergo a dramatic reorganization of their processes shortly after they migrate to their appropriate laminar position. This is an important process because it is now understood that the apical processes are important for establishing the regular mosaic of horizontal cells in the retina and proper reorganization during lamination is required for synaptogenesis with photoreceptors and bipolar neurons. However, this process is difficult to study because the analysis of horizontal neuron anatomy is labor intensive and time-consuming. In this paper, we present a computational method for automatically tracing the three-dimensional (3-D) dendritic structure of horizontal retinal neurons in two-photon laser scanning microscope (TPLSM) imagery. Our method is based on 3-D skeletonization and is thus able to preserve the complex structure of the dendritic arbor of these cells. We demonstrate the effectiveness of our approach by comparing our tracing results against two sets of semi-automated traces over a set of 10 horizontal neurons ranging in age from P1 to P5. We observe an average agreement level of 81% between our automated trace and the manual traces. This automated method will serve as an important starting point for further refinement and optimization.