Macular: a multi-scale simulation platform for the retina and the primary visual system

TL;DR

Macular is a versatile simulation platform with a graphical interface for modeling the retina and visual cortex, enabling in silico experiments with customizable structures, inputs, and parameters for neurobiologists and modelers.

Contribution

It introduces a user-friendly, graphical simulation environment for the retina and visual system, allowing hypothesis testing without programming expertise.

Findings

Supports complex multi-layer 3D structures

Enables simulation of various physiological and pathological conditions

Provides customizable cell and synapse models

Abstract

We developed Macular, a simulation platform with a graphical interface, designed to produce in silico experiment scenarios for the retina and the primary visual system. A scenario consists of generating a three-dimensional structure with interconnected layers, each layer corresponding to a type of 'cell' in the retina or visual cortex. The cells can correspond to neurons or more complex structures (such as cortical columns). The inputs are arbitrary videos. The user can use the cells and synapses provided with the software, or create their own using a graphical interface where they enter the constituent equations in text format (e.g., LaTeX). They also create the three-dimensional structure via the graphical interface. Macular then automatically generates and compiles the C++ code and generates the simulation interface. This allows the user to view the input video and the three-dimensional structure in layers. It also allows the user to select cells and synapses in each layer and view the activity of their state variables. Finally, the user can adjust the phenomenological parameters of the cells or synapses via the interface. We provide several example scenarios, corresponding to published articles, including an example of a retino-cortical model. Macular was designed for neurobiologists and modelers, specialists in the primary visual system, who want to test hypotheses in silico without the need for programming. By design, this tool allows natural or altered conditions (pharmacology, pathology, development) to be simulated.