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.
Abstract-A large number of neural network models are based on a feedforward topology (perceptrons, backpropagation networks, radial basis functions, support vector machines, etc.), thus lacking dynamics. In such networks, the order of input presentation is meaningless (i.e., it does not affect the behavior) since the behavior is largely reactive. That is, such neural networks can only operate in the present, having no access to the past or the future. However, biological neural networks are mostly constructed with a recurrent topology, and recurrent (artificial) neural network models are able to exhibit rich temporal dynamics, thus time becomes an essential factor in their operation. In this paper, we will investigate the emergence of recollection and prediction in evolving neural networks. First, we will show how reactive, feedforward networks can evolve a memory-like function (recollection) through utilizing external markers dropped and detected in the environment. Second, we will investigate how recurrent networks with more predictable internal state trajectory can emerge as an eventual winner in evolutionary struggle when competing networks with less predictable trajectory show the same level of behavioral performance. We expect our results to help us better understand the evolutionary origin of recollection and prediction in neuronal networks, and better appreciate the role of time in brain function.
The function of the brain is intricately woven into the fabric of time. Functions such as (1) storing and accessing past memories, (2) dealing with immediate sensorimotor needs in the present, and (3) projecting into the future for goal-directed behavior are good examples of how key brain processes are integrated into time. Moreover, it can even seem that the brain generates time (in the psychological sense, not in the physical sense) since, without the brain, a living organism cannot have the notion of past nor future. When combined with an evolutionary perspective, this seemingly straight-forward idea that the brain enables the conceptualization of past and future can lead to deeper insights into the principles of brain function, including that of consciousness. In this paper, we systematically investigate, through simulated evolution of artificial neural networks, conditions for the emergence of past and future in simple neural architectures, and discuss the implications of our findings for consciousness and mind uploading.
In this paper, we will review a novel microscopy modality called Knife-Edge Scanning Microscopy (KESM) that we have developed over the past twelve years (since 1999) and discuss its relevance to connectomics and neural networks research. The operational principle of KESM is to simultaneously section and image small animal brains embedded in hard polymer resin so that a near-isotropic, sub-micrometer voxel size of 0.6 µm × 0.7 µm × 1.0 µm can be achieved over ∼1 cm 3 volume of tissue which is enough to hold an entire mouse brain. At this resolution, morphological details such as dendrites, dendritic spines, and axons are visible (for sparse stains like Golgi). KESM has been successfully used to scan whole mouse brains stained in Golgi (neuronal morphology), Nissl (somata), and India ink (vasculature), providing unprecedented insights into the system-level architectural layout of microstructures within the mouse brain. In this paper, we will present whole-brain-scale data sets from KESM and discuss challenges and opportunities posed to connectomics and neural networks research by such detailed yet system-level data.
What is time? Since the function of the brain is closely tied in with that of time, investigating the origin of time in the brain can help shed light on this question. In this paper, we propose to use simulated evolution of artificial neural networks to investigate the relationship between time and brain function, and the evolution of time in the brain. A large number of neural network models are based on a feedforward topology (perceptrons, backpropagation networks, radial basis functions, support vector machines, etc.), thus lacking dynamics. In such networks, the order of input presentation is meaningless (i.e., it does not affect the behavior) since the behavior is largely reactive. That is, such neural networks can only operate in the present, having no access to the past or the future. However, biological neural networks are mostly constructed with a recurrent topology, and recurrent (artificial) neural network models are able to exhibit rich temporal dynamics, thus time becomes an essential factor in their operation. In this paper, we will investigate the emergence of recollection and prediction in evolving neural networks. First, we will show how reactive, feedforward networks can evolve a memory-like function (rec- Chung, Kwon, Mann, and Choe ollection) through utilizing external markers dropped and detected in the environment. Second, we will investigate how recurrent networks with more predictable internal state trajectory can emerge as an eventual winner in evolutionary struggle when competing networks with less predictable trajectory show the same level of behavioral performance. We expect our results to help us better understand the evolutionary origin of recollection and prediction in neuronal networks, and better appreciate the role of time in brain function.
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