A graphical, scalable and intuitive method for the placement and the connection of biological cells

We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the identity of the different structures and the alpha channel indicates the local cell density, this method guarantees a discrete distribution of cell position respecting the local density function. This method scales to any number of cells, allows to specify several different structures at once with arbitrary shapes and provides a scalable and versatile alternative to the more classical assumption of a uniform non-spatial distribution. Furthermore, several connection schemes can be derived from the paired distances between cells using either an automatic mapping or a user-defined local reference frame, providing new computational properties for the underlying model. The method is illustrated on a discrete homogeneous neural field, on the distribution of cones and rods in the retina and on a coronal view of the basal ganglia.Comment: Corresponding code at https://github.com/rougier/spatial-computatio

A Computational Model of Spatial Memory Anticipation during Visual Search

Some visual search tasks require to memorize the location of stimuli that have been previously scanned. Considerations about the eye movements raise the question of how we are able to maintain a coherent memory, despite the frequent drastically changes in the perception. In this article, we present a computational model that is able to anticipate the consequences of the eye movements on the visual perception in order to update a spatial memor

A computational approach to the covert and overt deployment of spatial attention

Popular computational models of visual attention tend to neglect the influence of saccadic eye movements whereas it has been shown that the primates perform on average three of them per seconds and that the neural substrate for the deployment of attention and the execution of an eye movement might considerably overlap. Here we propose a computational model in which the deployment of attention with or without a subsequent eye movement emerges from local, distributed and numerical computations

Structure of receptive fields in a computational model of area 3b of primary sensory cortex

International audienceIn a previous work, we introduced a computational model of area 3b which is built upon the neural field theory and receives input from a simplified model of the index distal finger pad populated by a random set of touch receptors (Merkell cells). This model has been shown to be able to self-organize following the random stimulation of the finger pad model and to cope, to some extent, with cortical or skin lesions. The main hypothesis of the model is that learning of skin representations occurs at the thalamo-cortical level while cortico-cortical connections serve a stereotyped competition mechanism that shapes the receptive fields. To further assess this hypothesis and the validity of the model, we reproduced in this article the exact experimental protocol of DiCarlo et al. that has been used to examine the structure of receptive fields in area 3b of the primary somatosensory cortex. Using the same analysis toolset, the model yields consistent results, having most of the receptive fields to contain a single region of excitation and one to several regions of inhibition. We further proceeded our study using a dynamic competition that deeply influences the formation of the receptive fields. We hypothesized this dynamic competition to correspond to some form of somatosensory attention that may help to precisely shape the receptive fields. To test this hypothesis, we designed a protocol where an arbitrary region of interest is delineated on the index distal finger pad and we either (1) instructed explicitly the model to attend to this region (simulating an attentional signal) (2) preferentially trained the model on this region or (3) combined the two aforementioned protocols simultaneously. Results tend to confirm that dynamic competition leads to shrunken receptive fields and its joint interaction with intensive training promotes a massive receptive fields migration and shrinkage

A regularization process to implement self-organizing neuronal networks

Kohonen Self-Organizing maps are interesting computational structures because of their original properties, including adaptive topology and competition, their biological plausibility and their successful applications to a variety of real-world applications. In this paper, this neuronal model is presented, together with its possible implementation with a variational approach. We then explain why, beyond the interest for understanding the visual cortex, this approach is also interesting for making easier and more efficient the choice of this neuronal technique for real-world applications

A dynamic neural field approach to the covert and overt deployment of spatial attention

International audienceAbstract The visual exploration of a scene involves the in- terplay of several competing processes (for example to se- lect the next saccade or to keep fixation) and the integration of bottom-up (e.g. contrast) and top-down information (the target of a visual search task). Identifying the neural mech- anisms involved in these processes and in the integration of these information remains a challenging question. Visual attention refers to all these processes, both when the eyes remain fixed (covert attention) and when they are moving (overt attention). Popular computational models of visual attention consider that the visual information remains fixed when attention is deployed while the primates are executing around three saccadic eye movements per second, changing abruptly this information. We present in this paper a model relying on neural fields, a paradigm for distributed, asyn- chronous and numerical computations and show that covert and overt attention can emerge from such a substratum. We identify and propose a possible interaction of four elemen- tary mechanisms for selecting the next locus of attention, memorizing the previously attended locations, anticipating the consequences of eye movements and integrating bottom- up and top-down information in order to perform a visual search task with saccadic eye movements

A Robust Model of Gated Working Memory

International audienceGated working memory is defined as the capacity of holding arbitrary information at any time in order to be used at a later time. Based on electrophysi-ological recordings, several computational models have tackled the problem using dedicated and explicit mechanisms. We propose instead to consider an implicit mechanism based on a random recurrent neural network. We introduce a robust yet simple reservoir model of gated working memory with instantaneous updates. The model is able to store an arbitrary real value at random time over an extended period of time. The dynamics of the model is a line attractor that learns to exploit reentry and a non-linearity during the training phase using only a few representative values. A deeper study of the model shows that there is actually a large range of hyper parameters for which the results hold (number of neurons, sparsity, global weight scaling, etc.) such that any large enough population, mixing excitatory and inhibitory neurons can quickly learn to realize such gated working memory. In a nutshell, with a minimal set of hypotheses, we show that we can have a robust model of working memory. This suggests this property could be an implicit property of any random population, that can be acquired through learning. Furthermore, considering working memory to be a physically open but functionally closed system, we give account on some counter-intuitive electrophysiological recordings

Glumpy: Fast, scalable and beautiful scientific visualization

International audienceGlumpy is a python library for scientific visualization that is both fast, scalable and beautiful. Glumpy offers an intuitive interface between numpy and modern OpenGL. Numpy arrays are tracked automatically such that any change on the CPU is reflected automatically on the GPU, making the integration seamless. glumpy provides more than 100 examples showing how to achieve this or that visualization, such as antialiasing, text rendering, isolines computation, image filtering, cartographic projection, realtime signals, FLUID simulation, SVG rendering, etc. interactive session using the regular python shell allows for dynamic data exploration

Antialiased 2D Grid, Marker, and Arrow Shaders

International audienceGrids, markers, and arrows are important components in scientific visualisation. Grids are widely used in scientific plots and help visually locate data. Markers visualize individual points and aggregated data. Quiver plots show vector fields, such as a velocity buffer, through regularly-placed arrows. Being able to draw these components quickly is critical if one wants to offer interactive visualisation. This article provides algorithms with GLSL implementations for drawing grids, markers, and arrows using implicit surfaces that make it possible quickly render pixel-perfect antialiased shapes