An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics

The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al

The world according to zebrafish: How neural circuits generate behaviour

Understanding how the brain functions is one of the most ambitious current scientific goals. This challenge will only be accomplish by a multidisciplinary approach involving genetics, molecular biology, optics, ethology, neurobiology and mathematics and using tractable model systems. The zebrafish larva is a transparent genetically tractable small vertebrate, ideal for the combination state-of-the- art imaging techniques (e.g. two-photon scanning microscopy, single-plane illumination microscopy, spatial light modulator microscopy and lightfield microscopy), bioluminiscence and optogenetics to monitor and manipulate neuronal activity from single specific neurons up to the entire brain, in an intact behaving organism. Furthermore, the zebrafish model offers large and increasing collection of mutant and transgenic lines modelling human brain diseases. With these advantages in hand, the zebrafish larva became in the recent years, a novel animal model to study neuronal circuits and behaviour, taking us closer than ever before to understand how the brain controls behaviour

A 2D virtual reality system for visual goal-driven navigation in zebrafish larvae

International audienceAnimals continuously rely on sensory feedback to adjust motor commands. In order to study the role of visual feedback in goal-driven navigation, we developed a 2D visual virtual reality system for zebrafish larvae. The visual feedback can be set to be similar to what the animal experiences in natural conditions. Alternatively, modification of the visual feedback can be used to study how the brain adapts to perturbations. For this purpose, we first generated a library of free-swimming behaviors from which we learned the relationship between the trajectory of the larva and the shape of its tail. Then, we used this technique to infer the intended displacements of head-fixed larvae, and updated the visual environment accordingly. Under these conditions, larvae were capable of aligning and swimming in the direction of a whole-field moving stimulus and produced the fine changes in orientation and position required to capture virtual prey. We demonstrate the sensitivity of larvae to visual feedback by updating the visual world in real-time or only at the end of the discrete swimming episodes. This visual feedback perturbation caused impaired performance of prey-capture behavior, suggesting that larvae rely on continuous visual feedback during swimming

Control of octopus arm extension by a peripheral motor program

For goal-directed arm movements, the nervous system generates a sequence of motor commands that bring the arm toward the target. Control of the octopus arm is especially complex because the arm can be moved in any direction, with a virtually infinite number of degrees of freedom. Here we show that arm extensions can be evoked mechanically or electrically in arms whose connection with the brain has been severed. These extensions show kinematic features that are almost identical to normal behavior, suggesting that the basic motor program for voluntary movement is embedded within the neural circuitry of the arm itself. Such peripheral motor programs represent considerable simplification in the motor control of this highly redundant appendage

A protocol for whole-brain Ca2+ imaging in Astyanax mexicanus, a model of comparative evolution

Summary: In this protocol, we describe a comparative approach to study the evolution of brain function in the Mexican tetra, Astyanax mexicanus. We developed surface fish and two independent populations of cavefish with pan-neuronal expression of the Ca2+ sensor GCaMP6s. We describe a methodology to prepare samples and image activity across the optic tectum and olfactory bulb. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics

The Emergence of the Spatial Structure of Tectal Spontaneous Activity Is Independent of Visual Inputs

International audienceGraphical Abstract Highlights d Development of tectal circuitry is influenced by the onset of retinal inputs d Enucleations impact the development of the tectum's spontaneous activity correlations d Enucleations only delay the topography of the correlated activity d In the absence of retinal inputs, the tectal circuitry is capable of predicting behavior In Brief The influence of retinal inputs on the development of the spontaneous neuronal activity of the tectal circuit is unknown. Pietri et al. show that retinal inputs are dispensable for the development of the spatial structure of spontaneous tectal activity, suggesting that the tectal circuit is preconfigured for its functional role