State-dependent pupil dilation rapidly shifts visual feature selectivity.

To increase computational flexibility, the processing of sensory inputs changes with behavioural context. In the visual system, active behavioural states characterized by motor activity and pupil dilation1,2 enhance sensory responses, but typically leave the preferred stimuli of neurons unchanged2-9. Here we find that behavioural state also modulates stimulus selectivity in the mouse visual cortex in the context of coloured natural scenes. Using population imaging in behaving mice, pharmacology and deep neural network modelling, we identified a rapid shift in colour selectivity towards ultraviolet stimuli during an active behavioural state. This was exclusively caused by state-dependent pupil dilation, which resulted in a dynamic switch from rod to cone photoreceptors, thereby extending their role beyond night and day vision. The change in tuning facilitated the decoding of ethological stimuli, such as aerial predators against the twilight sky10. For decades, studies in neuroscience and cognitive science have used pupil dilation as an indirect measure of brain state. Our data suggest that, in addition, state-dependent pupil dilation itself tunes visual representations to behavioural demands by differentially recruiting rods and cones on fast timescales.

Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks.

Responses to natural stimuli in area V4-a mid-level area of the visual ventral stream-are well predicted by features from convolutional neural networks (CNNs) trained on image classification. This result has been taken as evidence for the functional role of V4 in object classification. However, we currently do not know if and to what extent V4 plays a role in solving other computational objectives. Here, we investigated normative accounts of V4 (and V1 for comparison) by predicting macaque single-neuron responses to natural images from the representations extracted by 23 CNNs trained on different computer vision tasks including semantic, geometric, 2D, and 3D types of tasks. We found that V4 was best predicted by semantic classification features and exhibited high task selectivity, while the choice of task was less consequential to V1 performance. Consistent with traditional characterizations of V4 function that show its high-dimensional tuning to various 2D and 3D stimulus directions, we found that diverse non-semantic tasks explained aspects of V4 function that are not captured by individual semantic tasks. Nevertheless, jointly considering the features of a pair of semantic classification tasks was sufficient to yield one of our top V4 models, solidifying V4's main functional role in semantic processing and suggesting that V4's selectivity to 2D or 3D stimulus properties found by electrophysiologists can result from semantic functional goals.

Simultaneous spike-time locking to multiple frequencies.

Locking of neural firing is ubiquitously observed in the brain and occurs when neurons fire at a particular phase or in synchronization with an external signal. Here we study in detail the locking of single neurons to multiple distinct frequencies at the example of p-type electroreceptor afferents in the electrosensory system of the weakly electric fish Apteronotus leptorhynchus (brown ghost knifefish). We find that electrosensory afferents and pyramidal cells in the electrosensory lateral line lobe (ELL) lock to multiple frequencies, including the electric organ discharge (EOD) frequency, beat, and stimulus itself. We identify key elements necessary for locking to multiple frequencies, study its limits, and provide concise mathematical models reproducing our main findings. Our findings provide another example of how rate and temporal codes can coexist and complement each other in single neurons and demonstrate that sensory coding in p-type electroreceptor afferents provides a much richer representation of the sensory environment than commonly assumed. Since the underlying mechanisms are not specific to the electrosensory system, our results could provide the basis for studying multiple frequency locking in other systems.NEW & NOTEWORTHY Locking of neuronal spikes to external and internal signals is a ubiquitous neurophysiological mechanism that has been extensively studied in several brain areas and species. Using experimental data from the electrosensory system and concise mathematical models, we analyze how a single neuron can simultaneously lock to multiple frequencies. Our findings demonstrate how temporal and rate codes can complement each other and lead to rich neuronal representations of sensory signals.

Tracking activity patterns of a multispecies community of gymnotiform weakly electric fish in their neotropical habitat without tagging.

Field studies on freely behaving animals commonly require tagging and often are focused on single species. Weakly electric fish generate a species- and individual-specific electric organ discharge (EOD) and therefore provide a unique opportunity for individual tracking without tagging. Here, we present and test tracking algorithms based on recordings with submerged electrode arrays. Harmonic structures extracted from power spectra provide fish identity. Localization of fish based on weighted averages of their EOD amplitudes is found to be more robust than fitting a dipole model. We apply these techniques to monitor a community of three species, Apteronotus rostratus, Eigenmannia humboldtii and Sternopygus dariensis, in their natural habitat in Darién, Panama. We found consistent upstream movements after sunset followed by downstream movements in the second half of the night. Extrapolations of these movements and estimates of fish density obtained from additional transect data suggest that some fish cover at least several hundreds of meters of the stream per night. Most fish, including E. humboldtii, were traversing the electrode array solitarily. From in situ measurements of the decay of the EOD amplitude with distance of individual animals, we estimated that fish can detect conspecifics at distances of up to 2 m. Our recordings also emphasize the complexity of natural electrosensory scenes resulting from the interactions of the EODs of different species. Electrode arrays thus provide an unprecedented window into the so-far hidden nocturnal activities of multispecies communities of weakly electric fish at an unmatched level of detail.

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.

Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here, we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprogramming as reflected by differential expression of ∼20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1, previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants.

Encoding of social signals in all three electrosensory pathways of Eigenmannia virescens.

Extracting complementary features in parallel pathways is a widely used strategy for a robust representation of sensory signals. Weakly electric fish offer the rare opportunity to study complementary encoding of social signals in all of its electrosensory pathways. Electrosensory information is conveyed in three parallel pathways: two receptor types of the tuberous (active) system and one receptor type of the ampullary (passive) system. Modulations of the fish's own electric field are sensed by these receptors and used in navigation, prey detection, and communication. We studied the neuronal representation of electric communication signals (called chirps) in the ampullary and the two tuberous pathways of Eigenmannia virescens. We first characterized different kinds of chirps observed in behavioral experiments. Since Eigenmannia chirps simultaneously drive all three types of receptors, we studied their responses in in vivo electrophysiological recordings. Our results demonstrate that different electroreceptor types encode different aspects of the stimuli and each appears best suited to convey information about a certain chirp type. A decoding analysis of single neurons and small populations shows that this specialization leads to a complementary representation of information in the tuberous and ampullary receptors. This suggests that a potential readout mechanism should combine information provided by the parallel processing streams to improve chirp detectability.

Temporal adaptation enhances efficient contrast gain control on natural images.

Divisive normalization in primary visual cortex has been linked to adaptation to natural image statistics in accordance to Barlow's redundancy reduction hypothesis. Using recent advances in natural image modeling, we show that the previously studied static model of divisive normalization is rather inefficient in reducing local contrast correlations, but that a simple temporal contrast adaptation mechanism of the half-saturation constant can substantially increase its efficiency. Our findings reveal the experimentally observed temporal dynamics of divisive normalization to be critical for redundancy reduction.

What is the limit of redundancy reduction with divisive normalization?

Divisive normalization has been proposed as a nonlinear redundancy reduction mechanism capturing contrast correlations. Its basic function is a radial rescaling of the population response. Because of the saturation of divisive normalization, however, it is impossible to achieve a fully independent representation. In this letter, we derive an analytical upper bound on the inevitable residual redundancy of any saturating radial rescaling mechanism.

The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos.

Understanding how biological visual systems process information is challenging due to the complex nonlinear relationship between neuronal responses and high-dimensional visual input. Artificial neural networks have already improved our understanding of this system by allowing computational neuroscientists to create predictive models and bridge biological and machine vision. During the Sensorium 2022 competition, we introduced benchmarks for vision models with static input (i.e. images). However, animals operate and excel in dynamic environments, making it crucial to study and understand how the brain functions under these conditions. Moreover, many biological theories, such as predictive coding, suggest that previous input is crucial for current input processing. Currently, there is no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we propose the Sensorium 2023 Benchmark Competition with dynamic input (https://www.sensorium-competition.net/). This competition includes the collection of a new large-scale dataset from the primary visual cortex of five mice, containing responses from over 38,000 neurons to over 2 hours of dynamic stimuli per neuron. Participants in the main benchmark track will compete to identify the best predictive models of neuronal responses for dynamic input (i.e. video). We will also host a bonus track in which submission performance will be evaluated on out-of-domain input, using withheld neuronal responses to dynamic input stimuli whose statistics differ from the training set. Both tracks will offer behavioral data along with video stimuli. As before, we will provide code, tutorials, and strong pre-trained baseline models to encourage participation. We hope this competition will continue to strengthen the accompanying Sensorium benchmarks collection as a standard tool to measure progress in large-scale neural system identification models of the entire mouse visual hierarchy and beyond.

Energy Guided Diffusion for Generating Neurally Exciting Images.

In recent years, most exciting inputs (MEIs) synthesized from encoding models of neuronal activity have become an established method to study tuning properties of biological and artificial visual systems. However, as we move up the visual hierarchy, the complexity of neuronal computations increases. Consequently, it becomes more challenging to model neuronal activity, requiring more complex models. In this study, we introduce a new attention readout for a convolutional data-driven core for neurons in macaque V4 that outperforms the state-of-the-art task-driven ResNet model in predicting neuronal responses. However, as the predictive network becomes deeper and more complex, synthesizing MEIs via straightforward gradient ascent (GA) can struggle to produce qualitatively good results and overfit to idiosyncrasies of a more complex model, potentially decreasing the MEI's model-to-brain transferability. To solve this problem, we propose a diffusion-based method for generating MEIs via Energy Guidance (EGG). We show that for models of macaque V4, EGG generates single neuron MEIs that generalize better across architectures than the state-of-the-art GA while preserving the within-architectures activation and requiring 4.7x less compute time. Furthermore, EGG diffusion can be used to generate other neurally exciting images, like most exciting natural images that are on par with a selection of highly activating natural images, or image reconstructions that generalize better across architectures. Finally, EGG is simple to implement, requires no retraining of the diffusion model, and can easily be generalized to provide other characterizations of the visual system, such as invariances. Thus EGG provides a general and flexible framework to study coding properties of the visual system in the context of natural images.

Bipartite invariance in mouse primary visual cortex.

A defining characteristic of intelligent systems, whether natural or artificial, is the ability to generalize and infer behaviorally relevant latent causes from high-dimensional sensory input, despite significant variations in the environment. To understand how brains achieve generalization, it is crucial to identify the features to which neurons respond selectively and invariantly. However, the high-dimensional nature of visual inputs, the non-linearity of information processing in the brain, and limited experimental time make it challenging to systematically characterize neuronal tuning and invariances, especially for natural stimuli. Here, we extended "inception loops" - a paradigm that iterates between large-scale recordings, neural predictive models, and in silico experiments followed by in vivo verification - to systematically characterize single neuron invariances in the mouse primary visual cortex. Using the predictive model we synthesized Diverse Exciting Inputs (DEIs), a set of inputs that differ substantially from each other while each driving a target neuron strongly, and verified these DEIs' efficacy in vivo. We discovered a novel bipartite invariance: one portion of the receptive field encoded phase-invariant texture-like patterns, while the other portion encoded a fixed spatial pattern. Our analysis revealed that the division between the fixed and invariant portions of the receptive fields aligns with object boundaries defined by spatial frequency differences present in highly activating natural images. These findings suggest that bipartite invariance might play a role in segmentation by detecting texture-defined object boundaries, independent of the phase of the texture. We also replicated these bipartite DEIs in the functional connectomics MICrONs data set, which opens the way towards a circuit-level mechanistic understanding of this novel type of invariance. Our study demonstrates the power of using a data-driven deep learning approach to systematically characterize neuronal invariances. By applying this method across the visual hierarchy, cell types, and sensory modalities, we can decipher how latent variables are robustly extracted from natural scenes, leading to a deeper understanding of generalization.

Pattern completion and disruption characterize contextual modulation in mouse visual cortex.

A key role of sensory processing is integrating information across space. Neuronal responses in the visual system are influenced by both local features in the receptive field center and contextual information from the surround. While center-surround interactions have been extensively studied using simple stimuli like gratings, investigating these interactions with more complex, ecologically-relevant stimuli is challenging due to the high dimensionality of the stimulus space. We used large-scale neuronal recordings in mouse primary visual cortex to train convolutional neural network (CNN) models that accurately predicted center-surround interactions for natural stimuli. These models enabled us to synthesize surround stimuli that strongly suppressed or enhanced neuronal responses to the optimal center stimulus, as confirmed by in vivo experiments. In contrast to the common notion that congruent center and surround stimuli are suppressive, we found that excitatory surrounds appeared to complete spatial patterns in the center, while inhibitory surrounds disrupted them. We quantified this effect by demonstrating that CNN-optimized excitatory surround images have strong similarity in neuronal response space with surround images generated by extrapolating the statistical properties of the center, and with patches of natural scenes, which are known to exhibit high spatial correlations. Our findings cannot be explained by theories like redundancy reduction or predictive coding previously linked to contextual modulation in visual cortex. Instead, we demonstrated that a hierarchical probabilistic model incorporating Bayesian inference, and modulating neuronal responses based on prior knowledge of natural scene statistics, can explain our empirical results. We replicated these center-surround effects in the multi-area functional connectomics MICrONS dataset using natural movies as visual stimuli, which opens the way towards understanding circuit level mechanism, such as the contributions of lateral and feedback recurrent connections. Our data-driven modeling approach provides a new understanding of the role of contextual interactions in sensory processing and can be adapted across brain areas, sensory modalities, and species.

Towards a Foundation Model of the Mouse Visual Cortex.

Understanding the brain's perception algorithm is a highly intricate problem, as the inherent complexity of sensory inputs and the brain's nonlinear processing make characterizing sensory representations difficult. Recent studies have shown that functional models-capable of predicting large-scale neuronal activity in response to arbitrary sensory input-can be powerful tools for characterizing neuronal representations by enabling high-throughput in silico experiments. However, accurately modeling responses to dynamic and ecologically relevant inputs like videos remains challenging, particularly when generalizing to new stimulus domains outside the training distribution. Inspired by recent breakthroughs in artificial intelligence, where foundation models-trained on vast quantities of data-have demonstrated remarkable capabilities and generalization, we developed a "foundation model" of the mouse visual cortex: a deep neural network trained on large amounts of neuronal responses to ecological videos from multiple visual cortical areas and mice. The model accurately predicted neuronal responses not only to natural videos but also to various new stimulus domains, such as coherent moving dots and noise patterns, underscoring its generalization abilities. The foundation model could also be adapted to new mice with minimal natural movie training data. We applied the foundation model to the MICrONS dataset: a study of the brain that integrates structure with function at unprecedented scale, containing nanometer-scale morphology, connectivity with >500,000,000 synapses, and function of >70,000 neurons within a ~1mm3 volume spanning multiple areas of the mouse visual cortex. This accurate functional model of the MICrONS data opens the possibility for a systematic characterization of the relationship between circuit structure and function. By precisely capturing the response properties of the visual cortex and generalizing to new stimulus domains and mice, foundation models can pave the way for a deeper understanding of visual computation.

Functional connectomics reveals general wiring rule in mouse visual cortex.

To understand how the brain computes, it is important to unravel the relationship between circuit connectivity and function. Previous research has shown that excitatory neurons in layer 2/3 of the primary visual cortex of mice with similar response properties are more likely to form connections. However, technical challenges of combining synaptic connectivity and functional measurements have limited these studies to few, highly local connections. Utilizing the millimeter scale and nanometer resolution of the MICrONS dataset, we studied the connectivity-function relationship in excitatory neurons of the mouse visual cortex across interlaminar and interarea projections, assessing connection selectivity at the coarse axon trajectory and fine synaptic formation levels. A digital twin model of this mouse, that accurately predicted responses to arbitrary video stimuli, enabled a comprehensive characterization of the function of neurons. We found that neurons with highly correlated responses to natural videos tended to be connected with each other, not only within the same cortical area but also across multiple layers and visual areas, including feedforward and feedback connections, whereas we did not find that orientation preference predicted connectivity. The digital twin model separated each neuron's tuning into a feature component (what the neuron responds to) and a spatial component (where the neuron's receptive field is located). We show that the feature, but not the spatial component, predicted which neurons were connected at the fine synaptic scale. Together, our results demonstrate the "like-to-like" connectivity rule generalizes to multiple connection types, and the rich MICrONS dataset is suitable to further refine a mechanistic understanding of circuit structure and function.

Distinct organization of two cortico-cortical feedback pathways.

Neocortical feedback is critical for attention, prediction, and learning. To mechanically understand its function requires deciphering its cell-type wiring. Recent studies revealed that feedback between primary motor to primary somatosensory areas in mice is disinhibitory, targeting vasoactive intestinal peptide-expressing interneurons, in addition to pyramidal cells. It is unknown whether this circuit motif represents a general cortico-cortical feedback organizing principle. Here we show that in contrast to this wiring rule, feedback between higher-order lateromedial visual area to primary visual cortex preferentially activates somatostatin-expressing interneurons. Functionally, both feedback circuits temporally sharpen feed-forward excitation eliciting a transient increase-followed by a prolonged decrease-in pyramidal cell activity under sustained feed-forward input. However, under feed-forward transient input, the primary motor to primary somatosensory cortex feedback facilitates bursting while lateromedial area to primary visual cortex feedback increases time precision. Our findings argue for multiple cortico-cortical feedback motifs implementing different dynamic non-linear operations.

Natural image coding in V1: how much use is orientation selectivity?

Orientation selectivity is the most striking feature of simple cell coding in V1 that has been shown to emerge from the reduction of higher-order correlations in natural images in a large variety of statistical image models. The most parsimonious one among these models is linear Independent Component Analysis (ICA), whereas second-order decorrelation transformations such as Principal Component Analysis (PCA) do not yield oriented filters. Because of this finding, it has been suggested that the emergence of orientation selectivity may be explained by higher-order redundancy reduction. To assess the tenability of this hypothesis, it is an important empirical question how much more redundancy can be removed with ICA in comparison to PCA or other second-order decorrelation methods. Although some previous studies have concluded that the amount of higher-order correlation in natural images is generally insignificant, other studies reported an extra gain for ICA of more than 100%. A consistent conclusion about the role of higher-order correlations in natural images can be reached only by the development of reliable quantitative evaluation methods. Here, we present a very careful and comprehensive analysis using three evaluation criteria related to redundancy reduction: In addition to the multi-information and the average log-loss, we compute complete rate-distortion curves for ICA in comparison with PCA. Without exception, we find that the advantage of the ICA filters is small. At the same time, we show that a simple spherically symmetric distribution with only two parameters can fit the data significantly better than the probabilistic model underlying ICA. This finding suggests that, although the amount of higher-order correlation in natural images can in fact be significant, the feature of orientation selectivity does not yield a large contribution to redundancy reduction within the linear filter bank models of V1 simple cells.

Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex.

Clones of excitatory neurons derived from a common progenitor have been proposed to serve as elementary information processing modules in the neocortex. To characterize the cell types and circuit diagram of clonally related excitatory neurons, we performed multi-cell patch clamp recordings and Patch-seq on neurons derived from Nestin-positive progenitors labeled by tamoxifen induction at embryonic day 10.5. The resulting clones are derived from two radial glia on average, span cortical layers 2-6, and are composed of a random sampling of transcriptomic cell types. We find an interaction between shared lineage and connection type: related neurons are more likely to be connected vertically across cortical layers, but not laterally within the same layer. These findings challenge the view that related neurons show uniformly increased connectivity and suggest that integration of vertical intra-clonal input with lateral inter-clonal input may represent a developmentally programmed connectivity motif supporting the emergence of functional circuits.

Engineering a Less Artificial Intelligence.

Despite enormous progress in machine learning, artificial neural networks still lag behind brains in their ability to generalize to new situations. Given identical training data, differences in generalization are caused by many defining features of a learning algorithm, such as network architecture and learning rule. Their joint effect, called "inductive bias," determines how well any learning algorithm-or brain-generalizes: robust generalization needs good inductive biases. Artificial networks use rather nonspecific biases and often latch onto patterns that are only informative about the statistics of the training data but may not generalize to different scenarios. Brains, on the other hand, generalize across comparatively drastic changes in the sensory input all the time. We highlight some shortcomings of state-of-the-art learning algorithms compared to biological brains and discuss several ideas about how neuroscience can guide the quest for better inductive biases by providing useful constraints on representations and network architecture.

Inception loops discover what excites neurons most using deep predictive models.

Finding sensory stimuli that drive neurons optimally is central to understanding information processing in the brain. However, optimizing sensory input is difficult due to the predominantly nonlinear nature of sensory processing and high dimensionality of the input. We developed 'inception loops', a closed-loop experimental paradigm combining in vivo recordings from thousands of neurons with in silico nonlinear response modeling. Our end-to-end trained, deep-learning-based model predicted thousands of neuronal responses to arbitrary, new natural input with high accuracy and was used to synthesize optimal stimuli-most exciting inputs (MEIs). For mouse primary visual cortex (V1), MEIs exhibited complex spatial features that occurred frequently in natural scenes but deviated strikingly from the common notion that Gabor-like stimuli are optimal for V1. When presented back to the same neurons in vivo, MEIs drove responses significantly better than control stimuli. Inception loops represent a widely applicable technique for dissecting the neural mechanisms of sensation.

Response to Comment on "Principles of connectivity among morphologically defined cell types in adult neocortex".

The critique of Barth et al centers on three points: (i) the completeness of our study is overstated; (ii) the connectivity matrix we describe is biased by technical limitations of our brain-slicing and multipatching methods; and (iii) our cell classification scheme is arbitrary and we have simply renamed previously identified interneuron types. We address these criticisms in our Response.