MACULAR: Numerical platform for large scale simulations of the retina in pathological conditions
Abstract
Macular is a simulation platform for the retina and the primary visual cortex (V1), designed to reproduce the response to visual stimuli, in normal vision conditions, or in altered conditions (pharmacology, pathology, development). Macular is organised into a layered structure that mimics the multi-layers organisation of the visual system. It is fed by visual inputs (movies) then processed by this multi-layer structure.
At the heart of Macular are objects called “Cells”, inspired by biological neurons, but more general. A “Cell” can also be a group of neurons of the same type, a neural field generated by a large number of neurons (for example a cortical column), or even an electrode in a retinal prosthesis. A Cell is defined by internal variables (evolving over time), internal parameters (adjusted by cursors), a dynamic evolution (described by a set of differential equations) and inputs. Inputs can come from an external visual scene or from other synaptically connected cells. Synapses are also Macular objects defined by specific variables, parameters, and equations. Cells of the same type are connected in layers according to a graph with a specific type of synapses (intra-layer connectivity). Cells of a different type can also be connected via synapses (inter-layer connectivity).
All the information concerning the types of Cells, their inputs, their synapses and the organization of the layers are stored in a file of type .mac (for “macular”) defining what we call a “scenario”. Different types of scenarios are offered to the user, which they can load and play, while modifying the parameters and viewing the variables. More generally, Macular is built around a central idea: its use and its graphical interface can evolve according to the user’s objectives, so, the user can design their own scenarios, i.e. define their own Cells, synapses, layers, using a specific template, the Macular Template Engine. This template, and more generally, Macular, has been designed so that the user do not need to use computer programming to run their simulations.
Although Macular targets simulations of the retina, it is not limited to it. It is designed to propose and test models of the visual system, where, for example, Cells represent cortical columns in a mean-field model. However, Macular is, by no way, intended to simulate the retina or the early visual system as a whole. Instead, it is designed to check hypotheses on specific aspects of the visual system, try and reproduce specific experiments in silico. It is a tool for modellers and experimentalists. Especially, one can play the same stimuli as experimentalists and then “record” the response of models of the visual system layers. This is why the notion of scenario built by the user is the central. From this perspective, note that generating a model or a scenario, requires to have a clear idea of the equations to use, their parameters, and last but not the least, a coherent set of physical units. Thus, proposing a realistic scenario requires an important phase of design that Macular is not going to do for the user.
For more detail see the Macular Documentation page https://macular.gitlabpages.inria.fr/macular/user_doc/Macular/main.html .
