Slow waves (SWs) are spatio-temporal patterns of cortical activity that occur both during natural sleep and anesthesia and are preserved across species. Even though electrophysiological recordings have been largely used to characterize brain states, they are limited in the spatial resolution and cannot target specific neuronal population. Recently, large-scale optical imaging techniques coupled with functional indicators overcame these restrictions, and new pipelines of analysis and novel approaches of SWs modelling are needed to extract relevant features of the spatio-temporal dynamics of SWs from these highly spatially resolved data-sets. Here we combined wide-field fluorescence microscopy and a transgenic mouse model expressing a calcium indicator (GCaMP6f) in excitatory neurons to study SW propagation over the meso-scale under ketamine anesthesia. We developed a versatile analysis pipeline to identify and quantify the spatio-temporal propagation of the SWs. Moreover, we designed a computational simulator based on a simple theoretical model, which takes into account the statistics of neuronal activity, the response of fluorescence proteins and the slow waves dynamics. The simulator was capable of synthesizing artificial signals that could reliably reproduce several features of the SWs observed in vivo, thus enabling a calibration tool for the analysis pipeline. Comparison of experimental and simulated data shows the robustness of the analysis tools and its potential to uncover mechanistic insights of the Slow Wave Activity (SWA).

Quantifying the amount, content and direction of communication between brain regions is key to understanding brain function. Traditional methods to analyze brain activity based on the Wiener-Granger causality principle quantify the overall information propagated by neural activity between simultaneously recorded brain regions, but do not reveal the information flow about specific features of interest (such as sensory stimuli). Here, we develop a new information theoretic measure termed Feature-specific Information Transfer (FIT), quantifying how much information about a specific feature flows between two regions. FIT merges the Wiener-Granger causality principle with information-content specificity. We first derive FIT and prove analytically its key properties. We then illustrate and test them with simulations of neural activity, demonstrating that FIT identifies, within the total information flowing between regions, the information that is transmitted about specific features. We then analyze three neural datasets obtained with different recording methods, magneto- and electro-encephalography, and spiking activity, to demonstrate the ability of FIT to uncover the content and direction of information flow between brain regions beyond what can be discerned with traditional anaytical methods. FIT can improve our understanding of how brain regions communicate by uncovering previously hidden feature-specific information flow.

Information theory has deeply influenced the conceptualization of brain information processing and is a mainstream framework for analyzing how neural networks in the brain process information to generate behavior. Information theory tools have been initially conceived and used to study how information about sensory variables is encoded by the activity of small neural populations. However, recent multivariate information theoretic advances have enabled addressing how information is exchanged across areas and used to inform behavior. Moreover, its integration with dimensionality-reduction techniques has enabled addressing information encoding and communication by the activity of large neural populations or many brain areas, as recorded by multichannel activity measurements in functional imaging and electrophysiology. Here, we provide a Multivariate Information in Neuroscience Toolbox (MINT) that combines these new methods with statistical tools for robust estimation from limited-size empirical datasets. We demonstrate the capabilities of MINT by applying it to both simulated and real neural data recorded with electrophysiology or calcium imaging, but all MINT functions are equally applicable to other brain-activity measurement modalities. We highlight the synergistic opportunities that combining its methods afford for reverse engineering of specific information processing and flow between neural populations or areas, and for discovering how information processing functions emerge from interactions between neurons or areas. MINT works on Linux, Windows and macOS operating systems, is written in MATLAB (requires MATLAB version 2018b or newer) and depends on 4 native MATLAB toolboxes. The calculation of one possible way to compute information redundancy requires the installation and compilation of C files (made available by us also as pre-compiled files). MINT is freely available at https://github.com/panzerilab/MINT with DOI doi.org/10.5281/zenodo.13998526 and operates under a GNU GPLv3 license.

The publication of Mainen and Sejnowski’s 1995 seminal paper strongly renewed interest in how spike timing contributes to the neural code. In the 3 decades since then, considerable experimental and theoretical research has investigated the timescales at which spike timing contributes to the neural code. Here we review theoretical and experimental research of the last 30 years aimed at defining conceptually and measuring operationally these timescales. By a critical review of the literature, we individuate six broad classes of timescales that have been conceptualized and operationalized: the maximal temporal precision of spiking that a neuron can achieve, the encoding time window (the time window containing the information-bearing spike times), the encoding timescale (the coarsest time resolution for measuring spikes without losing information), the maximal discrimination precision timescale (the smallest spike time difference that can be discriminated behaviorally), the encoding-readout intersection timescale (the maximal timing precision at which stimulus information encoded in neural activity is also actually read out to inform behavior), and the information consistency timescale (measuring the stability of information encoding over time). Together, this work has revealed short and long timescales that influence information coding and affect behavior. Short encoding timescales, from milliseconds to tens of milliseconds, are useful for sensory information encoding and perception. Long consistency timescales, ranging from hundreds of milliseconds to seconds, are useful for accumulating evidence and stabilizing decisions.

Decision-makers often process new evidence selectively, depending on their current beliefs about the world. We asked whether such confirmation biases result from biases in the encoding of sensory evidence in the brain, or alternatively in the utilization of encoded evidence for behavior. Human participants estimated the source of a sequence of visual-spatial evidence samples while we measured cortical population activity with magnetoencephalography. Halfway through the sequence, participants were prompted to judge the more likely source category. We find that processing of subsequent evidence depends on its consistency with the previously chosen category. Evidence encoded in parietal cortex contributes more to the estimation report when that evidence is consistent with the previous choice compared to when it contradicts that choice. Our results indicate that information contradicting pre-existing beliefs has little impact on subsequent behavior, despite being precisely encoded in the brain. This provides room for deliberative control to counteract confirmation biases.