Comparative Study on Simulated Outdoor Navigation for Agricultural Robots.

This research presents a comprehensive comparative analysis of SLAM algorithms and Deep Neural Network (DNN)-based Behavior Cloning (BC) navigation in outdoor agricultural environments. The study categorizes SLAM algorithms into laser-based and vision-based approaches, addressing the specific challenges posed by uneven terrain and the similarity between aisles in an orchard farm. The DNN-based BC navigation technique proves efficient, exhibiting reduced human intervention and providing a viable alternative for agricultural navigation. Despite the DNN-based BC navigation approach taking more time to reach its target due to a constant throttle limit for steady speed, the overall performance in terms of driving deviation and human intervention is notable compared to conventional SLAM algorithms. We provide comprehensive evaluation criteria for selecting optimal techniques for outdoor agricultural navigations. The algorithms were tested in three different scenarios: Precision, Speed, and Autonomy. Our proposed performance metric, P, is weighted and normalized. The DNN-based BC algorithm showed the best performance among the others, with a performance of 0.92 in the Precision and Autonomy scenarios. When Speed is more important, the RTAB-Map showed the best score with 0.96. In a case where Autonomy has a higher priority, Gmapping also showed a comparable performance of 0.92 with the DNN-based BC.

Comparative Study of Markerless Vision-Based Gait Analyses for Person Re-Identification.

The model-based gait analysis of kinematic characteristics of the human body has been used to identify individuals. To extract gait features, spatiotemporal changes of anatomical landmarks of the human body in 3D were preferable. Without special lab settings, 2D images were easily acquired by monocular video cameras in real-world settings. The 2D and 3D locations of key joint positions were estimated by the 2D and 3D pose estimators. Then, the 3D joint positions can be estimated from the 2D image sequences in human gait. Yet, it has been challenging to have the exact gait features of a person due to viewpoint variance and occlusion of body parts in the 2D images. In the study, we conducted a comparative study of two different approaches: feature-based and spatiotemporal-based viewpoint invariant person re-identification using gait patterns. The first method is to use gait features extracted from time-series 3D joint positions to identify an individual. The second method uses a neural network, a Siamese Long Short Term Memory (LSTM) network with the 3D spatiotemporal changes of key joint positions in a gait cycle to classify an individual without extracting gait features. To validate and compare these two methods, we conducted experiments with two open datasets of the MARS and CASIA-A datasets. The results show that the Siamese LSTM outperforms the gait feature-based approaches on the MARS dataset by 20% and 55% on the CASIA-A dataset. The results show that feature-based gait analysis using 2D and 3D pose estimators is premature. As a future study, we suggest developing large-scale human gait datasets and designing accurate 2D and 3D joint position estimators specifically for gait patterns. We expect that the current comparative study and the future work could contribute to rehabilitation study, forensic gait analysis and early detection of neurological disorders.

Tracing Tubular Structures from Teravoxel-Sized Microscope Images.

Tracing vasculature and neurites from teravoxel sized light-microscopy data-sets is a challenge impeding the availability of processed data to the research community. This is because (1) Holding terabytes of data during run-time is not easy for a regular PC. (2) Processing all the data at once would be slow and inefficient. In this paper, we propose a way to mitigate this challenge by Divide Conquer and Combine (DCC) method. We first split the volume into many smaller and manageable sub-volumes before tracing. These sub-volumes can then be traced individually in parallel (or otherwise). We propose an algorithm to stitch together the traced data from these sub-volumes. This algorithm is robust and handles challenging scenarios like (1) sub-optimal tracing at edges (2) densely packed structures and (3) different depths of trace termination. We validate our results using whole mouse brain vasculature data-set obtained from the Knife-Edge Scanning Microscopy (KESM) based automated tissue scanner.

Predictable internal brain dynamics in EEG and its relation to conscious states.

Consciousness is a complex and multi-faceted phenomenon defying scientific explanation. Part of the reason why this is the case is due to its subjective nature. In our previous computational experiments, to avoid such a subjective trap, we took a strategy to investigate objective necessary conditions of consciousness. Our basic hypothesis was that predictive internal dynamics serves as such a condition. This is in line with theories of consciousness that treat retention (memory), protention (anticipation), and primary impression as the tripartite temporal structure of consciousness. To test our hypothesis, we analyzed publicly available sleep and awake electroencephalogram (EEG) data. Our results show that EEG signals from awake or rapid eye movement (REM) sleep states have more predictable dynamics compared to those from slow-wave sleep (SWS). Since awakeness and REM sleep are associated with conscious states and SWS with unconscious or less consciousness states, these results support our hypothesis. The results suggest an intricate relationship among prediction, consciousness, and time, with potential applications to time perception and neurorobotics.

Fast macro-scale transmission imaging of microvascular networks using KESM.

Accurate microvascular morphometric information has significant implications in several fields, including the quantification of angiogenesis in cancer research, understanding the immune response for neural prosthetics, and predicting the nature of blood flow as it relates to stroke. We report imaging of the whole mouse brain microvascular system at resolutions sufficient to perform accurate morphometry. Imaging was performed using Knife-Edge Scanning Microscopy (KESM) and is the first example of this technique that can be directly applied to clinical research. We are able to achieve ≈ 0.7µm resolution laterally with 1µm depth resolution using serial sectioning. No alignment was necessary and contrast was sufficient to allow segmentation and measurement of vessels.

Specimen preparation, imaging, and analysis protocols for knife-edge scanning microscopy.

Major advances in high-throughput, high-resolution, 3D microscopy techniques have enabled the acquisition of large volumes of neuroanatomical data at submicrometer resolution. One of the first such instruments producing whole-brain-scale data is the Knife-Edge Scanning Microscope (KESM), developed and hosted in the authors' lab. KESM has been used to section and image whole mouse brains at submicrometer resolution, revealing the intricate details of the neuronal networks (Golgi), vascular networks (India ink), and cell body distribution (Nissl). The use of KESM is not restricted to the mouse nor the brain. We have successfully imaged the octopus brain, mouse lung, and rat brain. We are currently working on whole zebra fish embryos. Data like these can greatly contribute to connectomics research; to microcirculation and hemodynamic research; and to stereology research by providing an exact ground-truth. In this article, we will describe the pipeline, including specimen preparation (fixing, staining, and embedding), KESM configuration and setup, sectioning and imaging with the KESM, image processing, data preparation, and data visualization and analysis. The emphasis will be on specimen preparation and visualization/analysis of obtained KESM data. We expect the detailed protocol presented in this article to help broaden the access to KESM and increase its utilization.

Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas.

Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions.

Facilitating neural dynamics for delay compensation: a road to predictive neural dynamics?

Goal-directed behavior is a hallmark of cognition. An important prerequisite to goal-directed behavior is that of prediction. In order to establish a goal and devise a plan, one needs to see into the future and predict possible future events. Our earlier work has suggested that compensation mechanisms for neuronal transmission delay may have led to a preliminary form of prediction. In that work, facilitating neuronal dynamics was found to be effective in overcoming delay (the Facilitating Activation Network model, or FAN). The extrapolative property of the delay compensation mechanism can be considered as prediction for incoming signals (predicting the present based on the past). The previous FAN model turns out to have a limitation especially when longer delay needs to be compensated, which requires higher facilitation rates than FAN's normal range. We derived an improved facilitating dynamics at the neuronal level to overcome this limitation. In this paper, we tested our proposed approach in controllers for 2D pole balancing, where the new approach was shown to perform better than the previous FAN model. Next, we investigated the differential utilization of facilitating dynamics in sensory vs. motor neurons and found that motor neurons utilize the facilitating dynamics more than the sensory neurons. These findings are expected to help us better understand the role of facilitating dynamics in delay compensation, and its potential development into prediction, a necessary condition for goal-directed behavior.