How Much Storage Precision Can Be Lost: Guidance for Near-Lossless Compression of Untargeted Metabolomics Mass Spectrometry Data

Several lossy compressors have achieved superior compression rates for mass spectrometry (MS) data at the cost of storage precision. Currently, the impacts of precision losses on MS data processing have not been thoroughly evaluated, which is critical for the future development of lossy compressors. We first evaluated different storage precision (32 bit and 64 bit) in lossless mzML files. We then applied 10 truncation transformations to generate precision-lossy files: five relative errors for intensities and five absolute errors for m/z values. MZmine3 and XCMS were used for feature detection and GNPS for compound annotation. Lastly, we compared Precision, Recall, F1 - score, and file sizes between lossy files and lossless files under different conditions. Overall, we revealed that the discrepancy between 32 and 64 bit precision was under 1%. We proposed an absolute m/z error of 10-4 and a relative intensity error of 2 × 10-2, adhering to a 5% error threshold (F1 - scores above 95%). For a stricter 1% error threshold (F1 - scores above 99%), an absolute m/z error of 2 × 10-5 and a relative intensity error of 2 × 10-3 were advised. This guidance aims to help researchers improve lossy compression algorithms and minimize the negative effects of precision losses on downstream data processing.

Neural mechanisms to incorporate visual counterevidence in self-movement estimation

In selecting appropriate behaviors, animals should weigh sensory evidence both for and against specific beliefs about the world. For instance, animals measure optic flow to estimate and control their own rotation. However, existing models of flow detection can be spuriously triggered by visual motion created by objects moving in the world. Here, we show that stationary patterns on the retina, which constitute evidence against observer rotation, suppress inappropriate stabilizing rotational behavior in the fruit fly Drosophila. In silico experiments show that artificial neural networks (ANNs) that are optimized to distinguish observer movement from external object motion similarly detect stationarity and incorporate negative evidence. Employing neural measurements and genetic manipulations, we identified components of the circuitry for stationary pattern detection, which runs parallel to the fly's local motion and optic-flow detectors. Our results show how the fly brain incorporates negative evidence to improve heading stability, exemplifying how a compact brain exploits geometrical constraints of the visual world.

IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA Proteomics

One of the key steps in data dependent acquisition (DDA) proteomics is detection of peptide isotopic clusters, also called "features", in MS1 spectra and matching them to MS/MS-based peptide identifications. A number of peptide feature detection tools became available in recent years, each relying on its own matching algorithm. Here, we provide an integrated solution, the intensity-based Quantitative Mix and Match Approach (IQMMA), which integrates a number of untargeted peptide feature detection algorithms and returns the most probable intensity values for the MS/MS-based identifications. IQMMA was tested using available proteomic data acquired for both well-characterized (ground truth) and real-world biological samples, including a mix of Yeast and E. coli digests spiked at different concentrations into the Human K562 digest used as a background, and a set of glioblastoma cell lines. Three open-source feature detection algorithms were integrated: Dinosaur, biosaur2, and OpenMS FeatureFinder. None of them was found optimal when applied individually to all the data sets employed in this work; however, their combined use in IQMMA improved efficiency of subsequent protein quantitation. The software implementing IQMMA is freely available at https://github.com/PostoenkoVI/IQMMA under Apache 2.0 license.

Proprioception gates visual object fixation in flying flies

Visual object tracking in animals as diverse as felines, frogs, and fish supports behaviors including predation, predator avoidance, and landscape navigation. Decades of experimental results show that a rigidly body-fixed tethered fly in a "virtual reality" visual flight simulator steers to follow the motion of a vertical bar, thereby "fixating" it on visual midline. This behavior likely reflects a desire to seek natural features such as plant stalks and has inspired algorithms for visual object tracking predicated on robust responses to bar velocity, particularly near visual midline. Using a modified flight simulator equipped with a magnetic pivot to allow frictionless turns about the yaw axis, we discovered that bar fixation as well as smooth steering responses to bar velocity are attenuated or eliminated in yaw-free conditions. Body-fixed Drosophila melanogaster respond to bar oscillation on a stationary ground with frequency-matched wing kinematics and fixate the bar on midline. Yaw-free flies respond to the same stimulus by ignoring the bar and maintaining their original heading. These differences are driven by proprioceptive signals, rather than visual signals, as artificially "clamping" a bar in the periphery of a yaw-free fly has no effect. When presented with a bar and ground oscillating at different frequencies, a yaw-free fly follows the frequency of the ground only, whereas a body-fixed fly robustly steers at the frequencies of both the bar and ground. Our findings support a model in which proprioceptive feedback promote active damping of high-gain optomotor responses to object motion.

Geological Borehole Video Image Stitching Method Based on Local Homography Matrix Offset Optimization

Due to the influence of the shooting environment and inherent image characteristics, there is a large amount of interference in the process of image stitching a geological borehole video. To accurately match the acquired image sequences in the inner part of a borehole, this paper presents a new method of stitching an unfolded borehole image, which uses the image generated from the video to construct a large-scale panorama. Firstly, the speeded-up robust feathers (SURF) algorithm is used to extract the image feature points and complete the rough matching. Then, the M-estimator sample consensus (MSAC) algorithm is introduced to remove the mismatched point pairs and obtain the homography matrix. Subsequently, we propose a local homography matrix offset optimization (LHOO) algorithm to obtain the optimal offset. Finally, the above process is cycled frame by frame, and the image sequence is continuously stitched to complete the construction of a cylindrical borehole panorama. The experimental results show that compared with those of the SIFT, Harris, ORB and SURF algorithms, the matching accuracy of our algorithm has been greatly improved. The final test is carried out on 225 consecutive video frames, and the panorama has a good visual effect, and the average time of each frame is 100 ms, which basically meets the requirements of the project.

Visual Analysis and Detection of Contrails in Aircraft Engine Simulations

Contrails are condensation trails generated from emitted particles by aircraft engines, which perturb Earth's radiation budget. Simulation modeling is used to interpret the formation and development of contrails. These simulations are computationally intensive and rely on high-performance computing solutions, and the contrail structures are not well defined. We propose a visual computing system to assist in defining contrails and their characteristics, as well as in the analysis of parameters for computer-generated aircraft engine simulations. The back-end of our system leverages a contrail-formation criterion and clustering methods to detect contrails' shape and evolution and identify similar simulation runs. The front-end system helps analyze contrails and their parameters across multiple simulation runs. The evaluation with domain experts shows this approach successfully aids in contrail data investigation.

Efficient Approach for Extracting High-Level B-Spline Features from LIDAR Data for Light-Weight Mapping

Light-weight and accurate mapping is made possible by high-level feature extraction from sensor readings. In this paper, the high-level B-spline features from a 2D LIDAR are extracted with a faster method as a solution to the mapping problem, making it possible for the robot to interact with its environment while navigating. The computation time of feature extraction is very crucial when mobile robots perform real-time tasks. In addition to the existing assessment measures of B-spline feature extraction methods, the paper also includes a new benchmark time metric for evaluating how well the extracted features perform. For point-to-point association, the most reliable vertex control points of the spline features generated from the hints of low-level point feature FALKO were chosen. The standard three indoor and one outdoor data sets were used for the experiment. The experimental results based on benchmark performance metrics, specifically computation time, show that the presented approach achieves better results than the state-of-the-art methods for extracting B-spline features. The classification of the methods implemented in the B-spline features detection and the algorithms are also presented in the paper.

Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results-especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes' rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated 'engine' capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

A new automatic stitching method for full-length lower limb radiography

Full-length lower limb x-rays are used to diagnose and plan surgical procedures, such as Total Knee Arthroplasty (TKA) and High Tibial Osteotomy (HTO). Due to the size limitation of digital radiography (DR), panoramic x-ray images cannot be obtained in a single exposure, necessitating multiple exposures and image stitching. In favor of manually constructing full-length x-ray images, we propose a new feature-based automated method for stitching together x-ray images. This new method is based on Canny algorithm, which detects and aligns bone edges before fusing them using a Wavelet form domain. Twenty-eight sets of lower limb x-ray images obtained from our hospital have been stitched and evaluated. The hip, knee, and ankle (HKA) angle was computed in two different ways then compared to manually stitched x-ray images by an expert. The stitching time was only three seconds, and the P-value was P = 0.974, and an accuracy rate of 100% was found. This method demonstrated greater precision and speed than both manually stitched x-ray images and previously published methods.

Analysis of Competition and Training Videos of Speed Climbing Athletes Using Feature and Human Body Keypoint Detection Algorithms

Compared to 25 years ago, the climbing sport itself has changed dramatically. From a rock climbing modification to a separation in three independent disciplines, the requirements to athletes and trainers increased rapidly. To ensure continuous improvement of the sport itself, the usage of measurement and sensor technology is unavoidable. Especially in the field of the discipline speed climbing, which will be performed as a single discipline at the Olympic Games 2024 in Paris, the current state of the art of movement analysis only consists of video analysis and the benefit of the experience of trainers. Therefore, this paper presents a novel method, which supports trainers and athletes and enables analysis of motion sequences and techniques. Prerecorded video footage is combined with existing feature and human body keypoint detection algorithms and standardized boundary conditions. Therefore, several image processing steps are necessary to convert the recorded movement of different speed climbing athletes to significant parameters for detailed analysis. By studying climbing trials of professional athletes and the used techniques in different sections of the speed climbing wall, the aim among others is to get comparable results and detect mistakes. As a conclusion, the presented method enables powerful analysis of speed climbing training and competition and serves with the aid of a user-friendly designed interface as a support for trainers and athletes for the evaluation of motion sequences.

Classification of certain vertebral degenerations using MRI image features

BACKGROUND AND OBJECTIVE

This article describes a fully automatic system for classifying various spinal degenerative phenotypes namely Modic changes, endplate defects and focal changes which are associated with lower back pain. These are obtained from T1/T2 Magnetic Resonance Imaging (MRI) scans. Lower back pain is a predominantly occurring ailment, which is prone to have various roots including the anatomical and pathophysciological aspects. Clinicians and radiologist use MRI to assess and evaluate the extent of damage, cause, and to decide on the future course of treatment. In large healthcare systems, to circumvent the manual reading of various image slices, we describe a system to automate the classification of various vertebral degeneracies that cause lower back pain.

METHODS

We implement a combination of feature extraction, image analysis based on geometry and classification using machine learning techniques for identifying vertebral degeneracies. Image features like local binary pattern, Hu's moments and gray level co-occurrence matrix (GLCM) based features are extracted to identify Modic changes, endplate defects, and presence of any focal changes. A combination of feature set is used for describing the extent of Modic change on the end plate. Feature sensitivity studies towards efficient classification is presented. A STIR based acute/chronic classification is also attempted in the current work.

RESULTS

The implemented method is tested and validated over a dataset containing 100 patients. The proposed framework for detecting the extent of Modic change achieves an accuracy of 85.91%. From the feature sensitivity analysis, it is revealed that entropy based measure obtained from gray level co-occurrence matrix alone is sufficient for detection of focal changes. The classification performance for detecting endplate defect is highly sensitive to the first 2 Hu's moments.

CONCLUSION

A novel approach to identify the allied vertebral degenerations and extent of Modic changes in vertebrae by exploiting image features and classification through machine learning is proposed. This shall assist radiologists in detecting abnormalities and in treatment planning.

Odour boosts visual object approach in flies

Multisensory integration is synergistic—input from one sensory modality might modulate the behavioural response to another. Work in flies has shown that a small visual object presented in the periphery elicits innate aversive steering responses in flight, likely representing an approaching threat. Object aversion is switched to approach when paired with a plume of food odour. The ‘open-loop’ design of prior work facilitated the observation of changing valence. How does odour influence visual object responses when an animal has naturally active control over its visual experience? In this study, we use closed-loop feedback conditions, in which a fly's steering effort is coupled to the angular velocity of the visual stimulus, to confirm that flies steer toward or ‘fixate’ a long vertical stripe on the visual midline. They tend either to steer away from or ‘antifixate’ a small object or to disengage active visual control, which manifests as uncontrolled object ‘spinning’ within this experimental paradigm. Adding a plume of apple cider vinegar decreases the probability of both antifixation and spinning, while increasing the probability of frontal fixation for objects of any size, including a normally typically aversive small object.

Inhibitory Interactions and Columnar Inputs to an Object Motion Detector in Drosophila

The direction-selective T4/T5 cells innervate optic-flow processing projection neurons in the lobula plate of the fly that mediate the visual control of locomotion. In the lobula, visual projection neurons coordinate complex behavioral responses to visual features, however, the input circuitry and computations that bestow their feature-detecting properties are less clear. Here, we study a highly specialized small object motion detector, LC11, and demonstrate that its responses are suppressed by local background motion. We show that LC11 expresses GABA-A receptors that serve to sculpt responses to small objects but are not responsible for the rejection of background motion. Instead, LC11 is innervated by columnar T2 and T3 neurons that are themselves highly sensitive to small static or moving objects, insensitive to wide-field motion and, unlike T4/T5, respond to both ON and OFF luminance steps.

Comfortable and Convenient Turning Skill Assessment for Alpine Skiers Using IMU and Plantar Pressure Distribution Sensors

Improving ski-turn skills is of interest to both competitive and recreational skiers, but it is not easy to improve on one’s own. Although studies have reported various methods of ski-turn skill evaluation, a simple method that can be used by oneself has not yet been established. In this study, we have proposed a comfortable method to assess ski-turn skills; this method enables skiers to easily understand the relationship between body control and ski motion. One expert skier and four intermediate skiers participated in this study. Small inertial measurement units (IMUs) and mobile plantar pressure distribution sensors were used to capture data while skiing, and three ski-turn features—ski motion, waist rotation, and how load is applied to the skis—as well as their symmetry, were assessed. The results showed that the motions of skiing and the waist in the expert skier were significantly larger than those in intermediate skiers. Additionally, we found that the expert skier only slightly used the heel to apply a load to the skis (heel load ratio: approximately 60%) and made more symmetrical turns than the intermediate skiers did. This study will provide a method for recreational skiers, in particular, to conveniently and quantitatively evaluate their ski-turn skills by themselves.

Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data

The evaluation of liquid chromatography high-resolution mass spectrometry (LC-HRMS) raw data is a crucial step in untargeted metabolomics studies to minimize false positive findings. A variety of commercial or open source software solutions are available for such data processing. This study aims to compare three different data processing workflows (Compound Discoverer 3.1, XCMS Online combined with MetaboAnalyst 4.0, and a manually programmed tool using R) to investigate LC-HRMS data of an untargeted metabolomics study. Simple but highly standardized datasets for evaluation were prepared by incubating pHLM (pooled human liver microsomes) with the synthetic cannabinoid A-CHMINACA. LC-HRMS analysis was performed using normal- and reversed-phase chromatography followed by full scan MS in positive and negative mode. MS/MS spectra of significant features were subsequently recorded in a separate run. The outcome of each workflow was evaluated by its number of significant features, peak shape quality, and the results of the multivariate statistics. Compound Discoverer as an all-in-one solution is characterized by its ease of use and seems, therefore, suitable for simple and small metabolomic studies. The two open source solutions allowed extensive customization but particularly, in the case of R, made advanced programming skills necessary. Nevertheless, both provided high flexibility and may be suitable for more complex studies and questions.

Retrospective CT/MRI Texture Analysis of Rapidly Progressive Hepatocellular Carcinoma

Rapidly progressive hepatocellular carcinoma (RPHCC) is a subset of hepatocellular carcinoma that demonstrates accelerated growth, and the radiographic features of RPHCC versus non-RPHCC have not been determined. The purpose of this retrospective study was to use baseline radiologic features and texture analysis for the accurate detection of RPHCC and subsequent improvement of clinical outcomes. We conducted a qualitative visual analysis and texture analysis, which selectively extracted and enhanced imaging features of different sizes and intensity variation including mean gray-level intensity (mean), standard deviation (SD), entropy, mean of the positive pixels (MPP), skewness, and kurtosis at each spatial scaling factor (SSF) value of RPHCC and non-RPHCC tumors in a computed tomography (CT) cohort of n = 11 RPHCC and n = 11 non-RPHCC and a magnetic resonance imaging (MRI) cohort of n = 13 RPHCC and n = 10 non-RPHCC. There was a statistically significant difference across visual CT irregular margins p = 0.030 and CT texture features in SSF between RPHCC and non-RPHCC for SSF-6, coarse-texture scale, mean p = 0.023, SD p = 0.053, MPP p = 0.023. A composite score of mean SSF-6 binarized + SD SSF-6 binarized + MPP SSF-6 binarized + irregular margins was significantly different between RPHCC and non-RPHCC (p = 0.001). A composite score ≥3 identified RPHCC with a sensitivity of 81.8% and specificity of 81.8% (AUC = 0.884, p = 0.002). CT coarse-texture-scale features in combination with visually detected irregular margins were able to statistically differentiate between RPHCC and non-RPHCC. By developing an image-based, non-invasive diagnostic criterion, we created a composite score that can identify RPHCC patients at their early stages when they are still eligible for transplantation, improving the clinical course of patient care.

Mobile Computing Technologies for Health and Mobility Assessment: Research Design and Results of the Timed Up and Go Test in Older Adults

Due to the increasing age of the European population, there is a growing interest in performing research that will aid in the timely and unobtrusive detection of emerging diseases. For such tasks, mobile devices have several sensors, facilitating the acquisition of diverse data. This study focuses on the analysis of the data collected from the mobile devices sensors and a pressure sensor connected to a Bitalino device for the measurement of the Timed-Up and Go test. The data acquisition was performed within different environments from multiple individuals with distinct types of diseases. Then this data was analyzed to estimate the various parameters of the Timed-Up and Go test. Firstly, the pressure sensor is used to extract the reaction and total test time. Secondly, the magnetometer sensors are used to identify the total test time and different parameters related to turning around. Finally, the accelerometer sensor is used to extract the reaction time, total test time, duration of turning around, going time, return time, and many other derived metrics. Our experiments showed that these parameters could be automatically and reliably detected with a mobile device. Moreover, we identified that the time to perform the Timed-Up and Go test increases with age and the presence of diseases related to locomotion.

Differences in Sodium Channel Densities in the Apical Dendrites of Pyramidal Cells of the Electrosensory Lateral Line Lobe

Heterogeneity of neural properties within a given neural class is ubiquitous in the nervous system and permits different sub-classes of neurons to specialize for specific purposes. This principle has been thoroughly investigated in the hindbrain of the weakly electric fish A. leptorhynchus in the primary electrosensory area, the Electrosensory Lateral Line lobe (ELL). The pyramidal cells (PCs) that receive inputs from tuberous electroreceptors are organized in three maps in distinct segments of the ELL. The properties of these cells vary greatly across maps due to differences in connectivity, receptor expression, and ion channel composition. These cells are a seminal example of bursting neurons and their bursting dynamic relies on the presence of voltage-gated Na⁺ channels in the extensive apical dendrites of the superficial PCs. Other ion channels can affect burst generation and their expression varies across ELL neurons and segments. For example, SK channels cause hyperpolarizing after-potentials decreasing the likelihood of bursting, yet bursting propensity is similar across segments. We question whether the depolarizing mechanism that generates the bursts presents quantitative differences across segments that could counterbalance other differences having the opposite effect. Although their presence and role are established, the distribution and density of the apical dendrites' Na⁺ channels have not been quantified and compared across ELL maps. Therefore, we test the hypothesis that Na⁺ channel density varies across segment by quantifying their distribution in the apical dendrites of immunolabeled ELL sections. We found the Na⁺ channels to be two-fold denser in the lateral segment (LS) than in the centro-medial segment (CMS), the centro-lateral segment (CLS) being intermediate. Our results imply that this differential expression of voltage-gated Na⁺ channels could counterbalance or interact with other aspects of neuronal physiology that vary across segments (e.g., SK channels). We argue that burst coding of sensory signals, and the way the network regulates bursting, should be influenced by these variations in Na⁺ channel density.

An Efficient and Geometric-Distortion-Free Binary Robust Local Feature

An efficient and geometric-distortion-free approach, namely the fast binary robust local feature (FBRLF), is proposed. The FBRLF searches the stable features from an image with the proposed multiscale adaptive and generic corner detection based on the accelerated segment test (MAGAST) to yield an optimum threshold value based on adaptive and generic corner detection based on the accelerated segment test (AGAST). To overcome the problem of image noise, the Gaussian template is applied, which is efficiently boosted by the adoption of an integral image. The feature matching is conducted by incorporating the voting mechanism and lookup table method to achieve a high accuracy with low computational complexity. The experimental results clearly demonstrate the superiority of the proposed method compared with the former schemes regarding local stable feature performance and processing efficiency.

[Processing of impedance cardiogram differential for non-invasive cardiac function detection]

The precise recognition of feature points of impedance cardiogram (ICG) is the precondition of calculating hemodynamic parameters based on thoracic bioimpedance. To improve the accuracy of detecting feature points of ICG signals, a new method was proposed to de-noise ICG signal based on the adaptive ensemble empirical mode decomposition and wavelet threshold firstly, and then on the basis of adaptive ensemble empirical mode decomposition, we combined difference and adaptive segmentation to detect the feature points, A, B, C and X, in ICG signal. We selected randomly 30 ICG signals in different forms from diverse cardiac patients to examine the accuracy of the proposed approach and the accuracy rate of the proposed algorithm is 99.72%. The improved accuracy rate of feature detection can help to get more accurate cardiac hemodynamic parameters on the basis of thoracic bioimpedance.

Automatic Processing Advantage of Cartoon Face in Internet Gaming Disorder: Evidence From P100, N170, P200, and MMN

Individuals with Internet gaming disorder (IGD) show deficits in face processing due to long-term Internet-game social activities based on cartoon faces in the popular online game "Strike of Kings." However, the abnormal neurocognitive mechanism of face recognition and processing in individuals with IGD has not been systematically explored. This study used event-related potential (ERP) methods and the reversed deviant-standard oddball paradigm to comprehensively compare four ERP components, namely, P100, N170, P200, and mismatch negativity (MMN), induced in the unconscious and automatic processing of realistic and cartoon faces in individuals with IGD. Results showed that, with respect to cartoon faces, individuals with IGD exhibited not only P100, P200 and MMN enhancements but also the absence of the N170 dominance effect in the left hemisphere. Our results also demonstrated that individuals with IGD had the advantages of early automatic perception of cartoon faces and automatic detection of changes in "cartoon" features. This study enhances our understanding of the mechanism of IGD from the neurocognitive perspective and provides candidate electrophysiological indicators for the clinical diagnosis of IGD.

A Peptide-Level Fully Annotated Data Set for Quantitative Evaluation of Precursor-Aware Mass Spectrometry Data Processing Algorithms

Modern label-free quantitative mass spectrometry workflows are complex experimental chains for devising the composition of biological samples. With benchtop and in silico experimental steps that each have a significant effect on the accuracy, coverage, and statistical significance of the study result, it is crucial to understand the efficacy and biases of each protocol decision. Although many studies have been conducted on wet lab experimental protocols, postacquisition data processing methods have not been adequately evaluated in large part due to a lack of available ground truth data. In this study, we provide a novel ground truth data set for mass spectrometry data analysis at the precursor (MS1) signal level comprised of isolated peptide signals from UPS2, a popular complex standard for proteomics analysis, requiring more than 1000 h of manual curation. The data set consists of more than 62 million points with 1,294,008 grouped into 57,518 extracted ion chromatograms and those grouped into 14,111 isotopic envelopes. This data set can be used to evaluate many aspects of mass spectrometry data processing, including precursor mapping and signal extraction algorithms.

High-Speed Videography Reveals How Honeybees Can Turn a Spatial Concept Learning Task Into a Simple Discrimination Task by Stereotyped Flight Movements and Sequential Inspection of Pattern Elements

Honey bees display remarkable visual learning abilities, providing insights regarding visual information processing in a miniature brain. It was discovered that bees can solve a task that is generally viewed as spatial concept learning in primates, specifically the concept of “above” and “below.” In these works, two pairs of visual stimuli were shown in the two arms of a Y-maze. Each arm displayed a “referent” shape (e.g., a cross, or a horizontal line) and a second geometric shape that appeared either above or below the referent. Bees learning the “concept of aboveness” had to choose the arm of the Y-maze in which a shape–any shape–occurred above the referent, while those learning the “concept of belowness” had to pick the arm in which there was an arbitrary item beneath the referent. Here, we explore the sequential decision-making process that allows bees to solve this task by analyzing their flight trajectories inside the Y-maze. Over 368 h of high-speed video footage of the bees' choice strategies were analyzed in detail. In our experiments, many bees failed the task, and, with the possible exception of a single forager, bees as a group failed to reach significance in picking the correct arm from the decision chamber of the maze. Of those bees that succeeded in choosing correctly, most required a close-up inspection of the targets. These bees typically employed a close-up scan of only the bottom part of the pattern before taking the decision of landing on a feeder. When rejecting incorrect feeders, they repeatedly scanned the pattern features, but were still, on average, faster at completing the task than the non-leaners. This shows that solving a concept learning task could actually be mediated by turning it into a more manageable discrimination task by some animals, although one individual in this study appeared to have gained the ability (by the end of the training) to solve the task in a manner predicted by concept learning.

A Spiking Neural Model of HT3D for Corner Detection

Obtaining good quality image features is of remarkable importance for most computer vision tasks. It has been demonstrated that the first layers of the human visual cortex are devoted to feature detection. The need for these features has made line, segment, and corner detection one of the most studied topics in computer vision. HT3D is a recent variant of the Hough transform for the combined detection of corners and line segments in images. It uses a 3D parameter space that enables the detection of segments instead of whole lines. This space also encloses canonical configurations of image corners, transforming corner detection into a pattern search problem. Spiking neural networks (SNN) have previously been proposed for multiple image processing tasks, including corner and line detection using the Hough transform. Following these ideas, this paper presents and describes in detail a model to implement HT3D as a Spiking Neural Network for corner detection. The results obtained from a thorough testing of its implementation using real images evince the correctness of the Spiking Neural Network HT3D implementation. Such results are comparable to those obtained with the regular HT3D implementation, which are in turn superior to other corner detection algorithms.

DETECTING FEATURES OF EPILEPTOGENESIS IN EEG AFTER TBI USING UNSUPERVISED DIFFUSION COMPONENT ANALYSIS

Epilepsy is among the most common serious disabling disorders of the brain, and the global burden of epilepsy exerts a tremendous cost to society. Most people with epilepsy have acquired forms, and the development of antiepileptogenic interventions could potentially prevent or cure these epilepsies [3, 13]. The discovery of potential antiepileptogenic treatments is currently a high research priority. Clinical validation would require a means to identify populations of patients at particular high risk for epilepsy after a potential epileptogenic insult to know when to treat and to document prevention or cure. We investigate the development of post-traumatic epilepsy (PTE) following traumatic brain injury (TBI), because this condition offers the best opportunity to know the time of onset of epileptogenesis in patients. Epileptogenesis is common after TBI, and because much is known about the physical history of PTE, it represents a near-ideal human model in which to study the process of developing seizures. Using scalp and depth EEG recordings for six patients, the goal of our analysis is to find a way to quantitatively detect features in the EEG that could potentially help predict seizure onset post trauma. Unsupervised Diffusion Component Analysis [5], a novel approach based on the diffusion mapping framework [4], reduces data dimensionality and provides pattern recognition that can be used to distinguish different states of the patient, such as seizures and non-seizure spikes in the EEG. This method is also adapted to the data to enable the extraction of the underlying brain activity. Previous work has shown that such techniques can be useful for seizure prediction [6]. Some new results that demonstrate how this algorithm is used to detect spikes in the EEG data as well as other changes over time are shown. This nonlinear and local network approach has been used to determine if the early occurrences of specific electrical features of epileptogenesis, such as interictal epileptiform activity and morphologic changes in spikes and seizures, during the initial week after TBI predicts the development of PTE.

Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing

Cryo-electron microscopy (cryo-EM) is a technique that produces three-dimensional density maps of large protein complexes. This allows for the study of the structure of these proteins. Identifying the secondary structures within proteins is vital to understanding the overall structure and function of the protein. The [Formula: see text]-barrel is one such secondary structure, commonly found in lipocalins and membrane proteins. In this article, we present a novel approach that utilizes genetic algorithms, kd-trees, and ray tracing to automatically detect and extract [Formula: see text]-barrels from cryo-EM density maps. This approach was tested on simulated and experimental density maps with zero, one, or multiple barrels in the density map. The results suggest that the proposed approach is capable of performing automatic detection of [Formula: see text]-barrels from medium resolution cryo-EM density maps.

Drosophila Spatiotemporally Integrates Visual Signals to Control Saccades

Like many visually active animals, including humans, flies generate both smooth and rapid saccadic movements to stabilize their gaze. How rapid body saccades and smooth movement interact for simultaneous object pursuit and gaze stabilization is not understood. We directly observed these interactions in magnetically tethered Drosophila free to rotate about the yaw axis. A moving bar elicited sustained bouts of saccades following the bar, with surprisingly little smooth movement. By contrast, a moving panorama elicited robust smooth movement interspersed with occasional optomotor saccades. The amplitude, angular velocity, and torque transients of bar-fixation saccades were finely tuned to the speed of bar motion and were triggered by a threshold in the temporal integral of the bar error angle rather than its absolute retinal position error. Optomotor saccades were tuned to the dynamics of panoramic image motion and were triggered by a threshold in the integral of velocity over time. A hybrid control model based on integrated motion cues simulates saccade trigger and dynamics. We propose a novel algorithm for tuning fixation saccades in flies.

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

Label-free quantification of shotgun LC–MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification (“FFId”), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between “internal” and “external” (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the “uncertain” feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards that provide a known ground-truth. The algorithm reached almost complete (>99%) quantification coverage for the full set of peptides identified at 1% FDR (PSM level). Compared with other software solutions for label-free quantification, this is an outstanding result, which was achieved at competitive quantification accuracy and reproducibility across replicates. The FDR for the feature selection was estimated at a low 1.5% on average per sample (3% for features inferred from external peptide IDs). The FFId software is open-source and freely available as part of OpenMS (www.openms.org).

Feature Detection in Visual Cortex during Different Functional States

Cortical activity exhibits distinct characteristics in different functional states. In awake behaving animals it shows less synchrony, while in rest or sleeping state cortical activity is most synchronous. Previous studies showed that switching between functional states can change the efficiency of flowing sensory information. Switching between functional states can be triggered by releasing neuromodulators which affect neurotransmitter release probability and depolarization of cortical neurons. In this work we focus on studying primary visual area V1, by using firing rate ring model with short-term synaptic depression (STD). We show that reconstruction of visual features from V1 activity depends on the functional state, with best precision achieved at the state with intermediate release probability. We suggest that this regime corresponds to the state of maximal visual attention.

Automated phenotype pattern recognition of zebrafish for high-throughput screening

Over the last years, the zebrafish (Danio rerio) has become a key model organism in genetic and chemical screenings. A growing number of experiments and an expanding interest in zebrafish research makes it increasingly essential to automatize the distribution of embryos and larvae into standard microtiter plates or other sample holders for screening, often according to phenotypical features. Until now, such sorting processes have been carried out by manually handling the larvae and manual feature detection. Here, a prototype platform for image acquisition together with a classification software is presented. Zebrafish embryos and larvae and their features such as pigmentation are detected automatically from the image. Zebrafish of 4 different phenotypes can be classified through pattern recognition at 72 h post fertilization (hpf), allowing the software to classify an embryo into 2 distinct phenotypic classes: wild-type versus variant. The zebrafish phenotypes are classified with an accuracy of 79-99% without any user interaction. A description of the prototype platform and of the algorithms for image processing and pattern recognition is presented.

The eyes have it

Molecular genetic experiments are revealing how the fly brain generates behavioral responses to visual stimuli.

Visual projection neurons in the Drosophila lobula link feature detection to distinct behavioral programs

Visual projection neurons (VPNs) provide an anatomical connection between early visual processing and higher brain regions. Here we characterize lobula columnar (LC) cells, a class of Drosophila VPNs that project to distinct central brain structures called optic glomeruli. We anatomically describe 22 different LC types and show that, for several types, optogenetic activation in freely moving flies evokes specific behaviors. The activation phenotypes of two LC types closely resemble natural avoidance behaviors triggered by a visual loom. In vivo two-photon calcium imaging reveals that these LC types respond to looming stimuli, while another type does not, but instead responds to the motion of a small object. Activation of LC neurons on only one side of the brain can result in attractive or aversive turning behaviors depending on the cell type. Our results indicate that LC neurons convey information on the presence and location of visual features relevant for specific behaviors.

MetMatch: A Semi-Automated Software Tool for the Comparison and Alignment of LC-HRMS Data from Different Metabolomics Experiments

Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented. The tool is implemented in the Java programming language, it features an intuitive user interface and its main goal is to facilitate the comparison of data obtained from different metabolomics experiments. Based on a feature list (i.e., processed LC-HRMS chromatograms with mass-to-charge ratio (m/z) values and retention times) that serves as a reference, the tool recognizes both m/z and retention time shifts of single or multiple analytical datafiles/batches of interest. MetMatch is also designed to account for differently formed ion species of detected metabolites. Corresponding ions and metabolites are matched and chromatographic peak areas, m/z values and retention times are combined into a single data matrix. The convenient user interface allows for easy manipulation of processing results and graphical illustration of the raw data as well as the automatically matched ions and metabolites. The software tool is exemplified with LC-HRMS data from untargeted metabolomics experiments investigating phenylalanine-derived metabolites in wheat and T-2 toxin/HT-2 toxin detoxification products in barley.

Comparing object recognition from binary and bipolar edge images for visual prostheses

Visual prostheses require an effective representation method due to the limited display condition which has only 2 or 3 levels of grayscale in low resolution. Edges derived from abrupt luminance changes in images carry essential information for object recognition. Typical binary (black and white) edge images have been used to represent features to convey essential information. However, in scenes with a complex cluttered background, the recognition rate of the binary edge images by human observers is limited and additional information is required. The polarity of edges and cusps (black or white features on a gray background) carries important additional information; the polarity may provide shape from shading information missing in the binary edge image. This depth information may be restored by using bipolar edges. We compared object recognition rates from 16 binary edge images and bipolar edge images by 26 subjects to determine the possible impact of bipolar filtering in visual prostheses with 3 or more levels of grayscale. Recognition rates were higher with bipolar edge images and the improvement was significant in scenes with complex backgrounds. The results also suggest that erroneous shape from shading interpretation of bipolar edges resulting from pigment rather than boundaries of shape may confound the recognition.

"Predictive Coding" Models of Plant Behavior

In this article we consider the possibility that plants exhibit anticipatory behavior, a mark of intelligence. If plants are able to anticipate and respond accordingly to varying states of their surroundings, as opposed to merely responding online to environmental contingencies, then such capacity may be in principle testable, and subject to empirical scrutiny. Our main thesis is that adaptive behavior can only take place by way of a mechanism that predicts the environmental sources of sensory stimulation. We propose to test for anticipation in plants experimentally by contrasting two empirical hypotheses: “feature detection” and “predictive coding.” We spell out what these contrasting hypotheses consist of by way of illustration from the animal literature, and consider how to transfer the rationale involved to the plant literature.

Burst Firing in the Electrosensory System of Gymnotiform Weakly Electric Fish: Mechanisms and Functional Roles

Neurons across sensory systems and organisms often display complex patterns of action potentials in response to sensory input. One example of such a pattern is the tendency of neurons to fire packets of action potentials (i.e., a burst) followed by quiescence. While it is well known that multiple mechanisms can generate bursts of action potentials at both the single-neuron and the network level, the functional role of burst firing in sensory processing is not so well understood to date. Here we provide a comprehensive review of the known mechanisms and functions of burst firing in processing of electrosensory stimuli in gymnotiform weakly electric fish. We also present new evidence from existing data showing that bursts and isolated spikes provide distinct information about stimulus variance. It is likely that these functional roles will be generally applicable to other systems and species.

Dinosaur: A Refined Open-Source Peptide MS Feature Detector

In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur.

Sequential Filtering Processes Shape Feature Detection in Crickets: A Framework for Song Pattern Recognition

Intraspecific acoustic communication requires filtering processes and feature detectors in the auditory pathway of the receiver for the recognition of species-specific signals. Insects like acoustically communicating crickets allow describing and analysing the mechanisms underlying auditory processing at the behavioral and neural level. Female crickets approach male calling song, their phonotactic behavior is tuned to the characteristic features of the song, such as the carrier frequency and the temporal pattern of sound pulses. Data from behavioral experiments and from neural recordings at different stages of processing in the auditory pathway lead to a concept of serially arranged filtering mechanisms. These encompass a filter for the carrier frequency at the level of the hearing organ, and the pulse duration through phasic onset responses of afferents and reciprocal inhibition of thoracic interneurons. Further, processing by a delay line and coincidence detector circuit in the brain leads to feature detecting neurons that specifically respond to the species-specific pulse rate, and match the characteristics of the phonotactic response. This same circuit may also control the response to the species-specific chirp pattern. Based on these serial filters and the feature detecting mechanism, female phonotactic behavior is shaped and tuned to the characteristic properties of male calling song.

Perception and Reality: Why a Wholly Empirical Paradigm is Needed to Understand Vision

A central puzzle in vision science is how perceptions that are routinely at odds with physical measurements of real world properties can arise from neural responses that nonetheless lead to effective behaviors. Here we argue that the solution depends on: (1) rejecting the assumption that the goal of vision is to recover, however imperfectly, properties of the world; and (2) replacing it with a paradigm in which perceptions reflect biological utility based on past experience rather than objective features of the environment. Present evidence is consistent with the conclusion that conceiving vision in wholly empirical terms provides a plausible way to understand what we see and why.

Will understanding vision require a wholly empirical paradigm?

Based on electrophysiological and anatomical studies, a prevalent conception is that the visual system recovers features of the world from retinal images to generate perceptions and guide behavior. This paradigm, however, is unable to explain why visual perceptions differ from physical measurements, or how behavior could routinely succeed on this basis. An alternative is that vision does not recover features of the world, but assigns perceptual qualities empirically by associating frequently occurring stimulus patterns with useful responses on the basis of survival and reproductive success. The purpose of the present article is to briefly describe this strategy of vision and the evidence for it.

Neurons forming optic glomeruli compute figure-ground discriminations in Drosophila

Many animals rely on visual figure-ground discrimination to aid in navigation, and to draw attention to salient features like conspecifics or predators. Even figures that are similar in pattern and luminance to the visual surroundings can be distinguished by the optical disparity generated by their relative motion against the ground, and yet the neural mechanisms underlying these visual discriminations are not well understood. We show in flies that a diverse array of figure-ground stimuli containing a motion-defined edge elicit statistically similar behavioral responses to one another, and statistically distinct behavioral responses from ground motion alone. From studies in larger flies and other insect species, we hypothesized that the circuitry of the lobula--one of the four, primary neuropiles of the fly optic lobe--performs this visual discrimination. Using calcium imaging of input dendrites, we then show that information encoded in cells projecting from the lobula to discrete optic glomeruli in the central brain group these sets of figure-ground stimuli in a homologous manner to the behavior; "figure-like" stimuli are coded similar to one another and "ground-like" stimuli are encoded differently. One cell class responds to the leading edge of a figure and is suppressed by ground motion. Two other classes cluster any figure-like stimuli, including a figure moving opposite the ground, distinctly from ground alone. This evidence demonstrates that lobula outputs provide a diverse basis set encoding visual features necessary for figure detection.

An excitatory amacrine cell detects object motion and provides feature-selective input to ganglion cells in the mouse retina

Retinal circuits detect salient features of the visual world and report them to the brain through spike trains of retinal ganglion cells. The most abundant ganglion cell type in mice, the so-called W3 ganglion cell, selectively responds to movements of small objects. Where and how object motion sensitivity arises in the retina is incompletely understood. In this study, we use 2-photon-guided patch-clamp recordings to characterize responses of vesicular glutamate transporter 3 (VGluT3)-expressing amacrine cells (ACs) to a broad set of visual stimuli. We find that these ACs are object motion sensitive and analyze the synaptic mechanisms underlying this computation. Anatomical circuit reconstructions suggest that VGluT3-expressing ACs form glutamatergic synapses with W3 ganglion cells, and targeted recordings show that the tuning of W3 ganglion cells' excitatory input matches that of VGluT3-expressing ACs' responses. Synaptic excitation of W3 ganglion cells is diminished, and responses to object motion are suppressed in mice lacking VGluT3. Object motion, thus, is first detected by VGluT3-expressing ACs, which provide feature-selective excitatory input to W3 ganglion cells.

DOI:http://dx.doi.org/10.7554/eLife.08025.001

Animals can use their eyes to detect moving objects, which helps them to avoid predators and other threats, and to spot potential prey or allies. Visual information from the eyes is sent to the brain, which processes the information to form a coherent picture of how the objects are moving. This processing has to be able to account for movements of the head, eyes, and body—which can cause the image of an object on the retina within the eye to move even if the object itself remains stationary.

Within the retina, light is converted into electrical signals by cells called rods and cones. A layer of cells called bipolar cells relay these signals to the ‘ganglion’ cells, which in turn pass them on to the brain. In mice, a type of ganglion cell called the W3 ganglion cell has been shown to respond selectively to small moving objects, but exactly how these cells acquire their motion sensitivity remained unclear.

Kim et al. now reveal that cells called amacrine cells, which regulate the transfer of signals from the bipolar cells to ganglion cells, supply the information needed for motion detection. The mouse eye contains up to 50 different types of amacrine cells. One of these—called the VG3-amacrine cell—increases its activity whenever an object moves relative to its background, but decreases its activity whenever the object and background move together. The overall effect is that the cells respond selectively to the presence of small moving objects.

Most amacrine cells regulate the transfer of signals within the retina by inhibiting the activity of ganglion cells. But, Kim et al. show that VG3-amacrine cells release a molecule called glutamate to activate W3 ganglion cells when a moving object is detected. These unusual and specialized cells are, thus, an essential component of a circuit in the nervous system that supports motion detection. It is possible that some other types of amacrine cells may also play specialized roles in the detection of other features in the visual world.

DOI:http://dx.doi.org/10.7554/eLife.08025.002

GridMass: a fast two-dimensional feature detection method for LC/MS

One of the initial and critical procedures for the analysis of metabolomics data using liquid chromatography and mass spectrometry is feature detection. Feature detection is the process to detect boundaries of the mass surface from raw data. It consists of detected abundances arranged in a two-dimensional (2D) matrix of mass/charge and elution time. MZmine 2 is one of the leading software environments that provide a full analysis pipeline for these data. However, the feature detection algorithms provided in MZmine 2 are based mainly on the analysis of one-dimension at a time. We propose GridMass, an efficient algorithm for 2D feature detection. The algorithm is based on landing probes across the chromatographic space that are moved to find local maxima providing accurate boundary estimations. We tested GridMass on a controlled marker experiment, on plasma samples, on plant fruits, and in a proteome sample. Compared with other algorithms, GridMass is faster and may achieve comparable or better sensitivity and specificity. As a proof of concept, GridMass has been implemented in Java under the MZmine 2 environment and is available at http://www.bioinformatica.mty.itesm.mx/GridMass and MASSyPup. It has also been submitted to the MZmine 2 developing community.

Automated analysis of courtship suppression learning and memory in Drosophila melanogaster

Study of the fruit fly, Drosophila melanogaster, has yielded important insights into the underlying molecular mechanisms of learning and memory. Courtship conditioning is a well-established behavioral assay used to study Drosophila learning and memory. Here, we describe the development of software to analyze courtship suppression assay data that correctly identifies normal or abnormal learning and memory traits of individual flies. Development of this automated analysis software will significantly enhance our ability to use this assay in large-scale genetic screens and disease modeling. The software increases the consistency, objectivity, and types of data generated.

Identification of peptide features in precursor spectra using Hardklör and Krönik

Hardklör and Krönik are software tools for feature detection and data reduction of high-resolution mass spectra. Hardklör is used to reduce peptide isotope distributions to a single monoisotopic mass and charge state, and can deconvolve overlapping peptide isotope distributions. Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). Both software tools contain a simple user interface and can be run from nearly any desktop computer. These tools are freely available from http://proteome.gs.washington.edu/software/hardklor.

Inhibition of SK and M channel-mediated currents by 5-HT enables parallel processing by bursts and isolated spikes

Although serotonergic innervation of sensory brain areas is ubiquitous, its effects on sensory information processing remain poorly understood. We investigated these effects in pyramidal neurons within the electrosensory lateral line lobe (ELL) of weakly electric fish. Surprisingly, we found that 5-HT is present at different levels across the different ELL maps; the presence of 5-HT fibers was highest in the map that processes intraspecies communication signals. Electrophysiological recordings revealed that 5-HT increased excitability and burst firing through a decreased medium afterhyperpolarization resulting from reduced small-conductance calcium-activated (SK) currents as well as currents mediated by an M-type potassium channel. We next investigated how 5-HT alters responses to sensory input. 5-HT application decreased the rheobase current, increased the gain, and decreased first spike latency. Moreover, it reduced discriminability between different stimuli, as quantified by the mutual information rate. We hypothesized that 5-HT shifts pyramidal neurons into a burst-firing mode where bursts, when considered as events, can detect the presence of particular stimulus features. We verified this hypothesis using signal detection theory. Our results indeed show that serotonin-induced bursts of action potentials, when considered as events, could detect specific stimulus features that were distinct from those detected by isolated spikes. Moreover, we show the novel result that isolated spikes transmit more information after 5-HT application. Our results suggest a novel function for 5-HT in that it enables differential processing by action potential patterns in response to current injection.

A general purpose feature extractor for light detection and ranging data

Feature extraction is a central step of processing Light Detection and Ranging (LIDAR) data. Existing detectors tend to exploit characteristics of specific environments: corners and lines from indoor (rectilinear) environments, and trees from outdoor environments. While these detectors work well in their intended environments, their performance in different environments can be poor. We describe a general purpose feature detector for both 2D and 3D LIDAR data that is applicable to virtually any environment. Our method adapts classic feature detection methods from the image processing literature, specifically the multi-scale Kanade-Tomasi corner detector. The resulting method is capable of identifying highly stable and repeatable features at a variety of spatial scales without knowledge of environment, and produces principled uncertainty estimates and corner descriptors at same time. We present results on both software simulation and standard datasets, including the 2D Victoria Park and Intel Research Center datasets, and the 3D MIT DARPA Urban Challenge dataset.

To burst or not to burst?

It is well known that some neurons tend to fire packets of action potentials followed by periods of quiescence (bursts) while others within the same stage of sensory processing fire in a tonic manner. However, the respective computational advantages of bursting and tonic neurons for encoding time varying signals largely remain a mystery. Weakly electric fish use cutaneous electroreceptors to convey information about sensory stimuli and it has been shown that some electroreceptors exhibit bursting dynamics while others do not. In this study, we compare the neural coding capabilities of tonically firing and bursting electroreceptor model neurons using information theoretic measures. We find that both bursting and tonically firing model neurons efficiently transmit information about the stimulus. However, the decoding mechanisms that must be used for each differ greatly: a non-linear decoder would be required to extract all the available information transmitted by the bursting model neuron whereas a linear one might suffice for the tonically firing model neuron. Further investigations using stimulus reconstruction techniques reveal that, unlike the tonically firing model neuron, the bursting model neuron does not encode the detailed time course of the stimulus. A novel measure of feature detection reveals that the bursting neuron signals certain stimulus features. Finally, we show that feature extraction and stimulus estimation are mutually exclusive computations occurring in bursting and tonically firing model neurons, respectively. Our results therefore suggest that stimulus estimation and feature extraction might be parallel computations in certain sensory systems rather than being sequential as has been previously proposed.

Spatiotemporal tuning of low-frequency cells in the anteroventral cochlear nucleus

Low-frequency cells in the anteroventral cochlear nucleus (AVCN) can be sensitive to changes in the spatiotemporal pattern of discharges across their auditory nerve (AN) inputs (). This sensitivity suggests that these cells may be tuned to particular spatiotemporal patterns, or features, in the discharge patterns of populations of AN fibers. To evaluate and characterize this sensitivity, we developed a technique whereby the physiological responses of AVCN cells to wide-band noise were analyzed using the simulated response of a population of AN fibers to the same noise stimulus. By averaging the simulated two-dimensional spatiotemporal pattern of AN activity that preceded each AVCN discharge, it was possible to derive a two-dimensional reverse-correlation function that characterized the spatiotemporal tuning of each AVCN cell. The derived spatiotemporal tuning pattern represented a feature in the AN population response that was most likely to precede discharges of the AVCN cell. To test the spatiotemporal tuning characterizations, we used these patterns to predict the responses of cells to noise stimuli statistically independent from the stimuli used to characterize the cells. This technique provides a general tool for the study of any neural system that involves the analysis of spatiotemporal input patterns.