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

TL;DR

Macular addresses the need for accessible, in silico modeling of the retina and early visual processing by providing a GUI-driven, multi-layer simulation platform that obviates programming for researchers. It integrates a template engine to define new cell and synapse models, supports realistic visual inputs and prosthetic stimulation, and offers both GUI and batch workflows across Linux, macOS, and Windows. The framework enables hypothesis testing across scales (retina to cortex) with configurable dynamics (ODE-based) and flexible connectivity, demonstrated through retinal waves and retino-cortical simulations. By combining an extensible architecture with real-time visualization and a library of predefined cells/synapses, Macular aims to accelerate hypothesis testing, development, and educational use in vision neuroscience, while remaining open-source for community-driven growth.

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.

Figures (3)

• Figure 1: The multi-layer structure of Macular. Here, we show a scenario involving three retinal layers and two cortical layers further described in section \ref{['Sec:Cortex']}. This scenario has been used in the papers emonet-cessac:25emonet-souihel-etal:25.
• Figure 2: The retinal waves scenario.Top left. Visualisation of the lattice evolution for the voltage of Starburst Amacrine Cells (SACs).Top right. Visualisation of the lattice evolution for the acetylcholine concentration produced by SACs. Bottom left. Time evolution for the voltage of a few SACs selected by the user. Bottom right. Time evolution for the acetylcholine production of a few SACs.
• Figure 3: The retino-cortical scenario. The upper left panel shows the heatmap of the 5 cell types. Bipolar cells with gain control appear in blue, amacrine in magenta, ganglion cells with gain control in yellow, excitatory population of cortical columns in green and inhibitory population of cortical columns in red. On the panel below, left, one sees the video of the stimulus, a white bar moving. Right panels are plots of Cells activity. The upper one displays retinal outputs : bipolar voltage (red), amacrine voltage (yellow) and ganglion cells firing rate (pink). The bottom panel displays cortical output : excitatory (blue) and inhibitory (orange) mean voltage.