Tachykinin-expressing neurons control male-specific aggressive arousal in Drosophila.

Males of most species are more aggressive than females, but the neural mechanisms underlying this dimorphism are not clear. Here, we identify a neuron and a gene that control the higher level of aggression characteristic of Drosophila melanogaster males. Males, but not females, contain a small cluster of FruM(+) neurons that express the neuropeptide tachykinin (Tk). Activation and silencing of these neurons increased and decreased, respectively, intermale aggression without affecting male-female courtship behavior. Mutations in both Tk and a candidate receptor, Takr86C, suppressed the effect of neuronal activation, whereas overexpression of Tk potentiated it. Tk neuron activation overcame reduced aggressiveness caused by eliminating a variety of sensory or contextual cues, suggesting that it promotes aggressive arousal or motivation. Tachykinin/Substance P has been implicated in aggression in mammals, including humans. Thus, the higher aggressiveness of Drosophila males reflects the sexually dimorphic expression of a neuropeptide that controls agonistic behaviors across phylogeny.

Automated measurement of mouse social behaviors using depth sensing, video tracking, and machine learning.

A lack of automated, quantitative, and accurate assessment of social behaviors in mammalian animal models has limited progress toward understanding mechanisms underlying social interactions and their disorders such as autism. Here we present a new integrated hardware and software system that combines video tracking, depth sensing, and machine learning for automatic detection and quantification of social behaviors involving close and dynamic interactions between two mice of different coat colors in their home cage. We designed a hardware setup that integrates traditional video cameras with a depth camera, developed computer vision tools to extract the body "pose" of individual animals in a social context, and used a supervised learning algorithm to classify several well-described social behaviors. We validated the robustness of the automated classifiers in various experimental settings and used them to examine how genetic background, such as that of Black and Tan Brachyury (BTBR) mice (a previously reported autism model), influences social behavior. Our integrated approach allows for rapid, automated measurement of social behaviors across diverse experimental designs and also affords the ability to develop new, objective behavioral metrics.

Sleep-spindle detection: crowdsourcing and evaluating performance of experts, non-experts and automated methods.

Sleep spindles are discrete, intermittent patterns of brain activity observed in human electroencephalographic data. Increasingly, these oscillations are of biological and clinical interest because of their role in development, learning and neurological disorders. We used an Internet interface to crowdsource spindle identification by human experts and non-experts, and we compared their performance with that of automated detection algorithms in data from middle- to older-aged subjects from the general population. We also refined methods for forming group consensus and evaluating the performance of event detectors in physiological data such as electroencephalographic recordings from polysomnography. Compared to the expert group consensus gold standard, the highest performance was by individual experts and the non-expert group consensus, followed by automated spindle detectors. This analysis showed that crowdsourcing the scoring of sleep data is an efficient method to collect large data sets, even for difficult tasks such as spindle identification. Further refinements to spindle detection algorithms are needed for middle- to older-aged subjects.

Functional identification of an aggression locus in the mouse hypothalamus.

Electrical stimulation of certain hypothalamic regions in cats and rodents can elicit attack behaviour, but the exact location of relevant cells within these regions, their requirement for naturally occurring aggression and their relationship to mating circuits have not been clear. Genetic methods for neural circuit manipulation in mice provide a potentially powerful approach to this problem, but brain-stimulation-evoked aggression has never been demonstrated in this species. Here we show that optogenetic, but not electrical, stimulation of neurons in the ventromedial hypothalamus, ventrolateral subdivision (VMHvl) causes male mice to attack both females and inanimate objects, as well as males. Pharmacogenetic silencing of VMHvl reversibly inhibits inter-male aggression. Immediate early gene analysis and single unit recordings from VMHvl during social interactions reveal overlapping but distinct neuronal subpopulations involved in fighting and mating. Neurons activated during attack are inhibited during mating, suggesting a potential neural substrate for competition between these opponent social behaviours.

Vision without the Image.

Novel image sensors transduce the stream of photons directly into asynchronous electrical pulses, rather than forming an image. Classical approaches to vision start from a good quality image and therefore it is tempting to consider image reconstruction as a first step to image analysis. We propose that, instead, one should focus on the task at hand (e.g., detection, tracking or control) and design algorithms that compute the relevant variables (class, position, velocity) directly from the stream of photons. We discuss three examples of such computer vision algorithms and test them on simulated data from photon-counting sensors. Such algorithms work just-in-time, i.e., they complete classification, search and tracking with high accuracy as soon as the information is sufficient, which is typically before there are enough photons to form a high-quality image. We argue that this is particularly useful when the photons are few or expensive, e.g., in astronomy, biological imaging, surveillance and night vision.

Decoding ventromedial hypothalamic neural activity during male mouse aggression.

The ventromedial hypothalamus, ventrolateral area (VMHvl) was identified recently as a critical locus for inter-male aggression. Optogenetic stimulation of VMHvl in male mice evokes attack toward conspecifics and inactivation of the region inhibits natural aggression, yet very little is known about its underlying neural activity. To understand its role in promoting aggression, we recorded and analyzed neural activity in the VMHvl in response to a wide range of social and nonsocial stimuli. Although response profiles of VMHvl neurons are complex and heterogeneous, we identified a subpopulation of neurons that respond maximally during investigation and attack of male conspecific mice and during investigation of a source of male mouse urine. These "male responsive" neurons in the VMHvl are tuned to both the inter-male distance and the animal's velocity during attack. Additionally, VMHvl activity predicts several parameters of future aggressive action, including the latency and duration of the next attack. Linear regression analysis further demonstrates that aggression-specific parameters, such as distance, movement velocity, and attack latency, can model ongoing VMHvl activity fluctuation during inter-male encounters. These results represent the first effort to understand the hypothalamic neural activity during social behaviors using quantitative tools and suggest an important role for the VMHvl in encoding movement, sensory, and motivation-related signals.

Speed versus accuracy in visual search: Optimal performance and neural architecture.

Searching for objects among clutter is a key ability of the visual system. Speed and accuracy are the crucial performance criteria. How can the brain trade off these competing quantities for optimal performance in different tasks? Can a network of spiking neurons carry out such computations, and what is its architecture? We propose a new model that takes input from V1-type orientation-selective spiking neurons and detects a target in the shortest time that is compatible with a given acceptable error rate. Subject to the assumption that the output of the primary visual cortex comprises Poisson neurons with known properties, our model is an ideal observer. The model has only five free parameters: the signal-to-noise ratio in a hypercolumn, the costs of false-alarm and false-reject errors versus the cost of time, and two parameters accounting for nonperceptual delays. Our model postulates two gain-control mechanisms--one local to hypercolumns and one global to the visual field--to handle variable scene complexity. Error rate and response time predictions match psychophysics data as we vary stimulus discriminability, scene complexity, and the uncertainty associated with each of these quantities. A five-layer spiking network closely approximates the optimal model, suggesting that known cortical mechanisms are sufficient for implementing visual search efficiently.

A number sense as an emergent property of the manipulating brain.

The ability to understand and manipulate numbers and quantities emerges during childhood, but the mechanism through which humans acquire and develop this ability is still poorly understood. We explore this question through a model, assuming that the learner is able to pick up and place small objects from, and to, locations of its choosing, and will spontaneously engage in such undirected manipulation. We further assume that the learner's visual system will monitor the changing arrangements of objects in the scene and will learn to predict the effects of each action by comparing perception with a supervisory signal from the motor system. We model perception using standard deep networks for feature extraction and classification. Our main finding is that, from learning the task of action prediction, an unexpected image representation emerges exhibiting regularities that foreshadow the perception and representation of numbers and quantity. These include distinct categories for zero and the first few natural numbers, a strict ordering of the numbers, and a one-dimensional signal that correlates with numerical quantity. As a result, our model acquires the ability to estimate numerosity, i.e. the number of objects in the scene, as well as subitization, i.e. the ability to recognize at a glance the exact number of objects in small scenes. Remarkably, subitization and numerosity estimation extrapolate to scenes containing many objects, far beyond the three objects used during training. We conclude that important aspects of a facility with numbers and quantities may be learned with supervision from a simple pre-training task. Our observations suggest that cross-modal learning is a powerful learning mechanism that may be harnessed in artificial intelligence.

Endotaxis: A neuromorphic algorithm for mapping, goal-learning, navigation, and patrolling.

An animal entering a new environment typically faces three challenges: explore the space for resources, memorize their locations, and navigate towards those targets as needed. Here we propose a neural algorithm that can solve all these problems and operates reliably in diverse and complex environments. At its core, the mechanism makes use of a behavioral module common to all motile animals, namely the ability to follow an odor to its source. We show how the brain can learn to generate internal "virtual odors" that guide the animal to any location of interest. This endotaxis algorithm can be implemented with a simple 3-layer neural circuit using only biologically realistic structures and learning rules. Several neural components of this scheme are found in brains from insects to humans. Nature may have evolved a general mechanism for search and navigation on the ancient backbone of chemotaxis.

A Foundation Model for Cell Segmentation.

Cells are a fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, most models in use are specialist models that work well for specific domains. Methods that have learned the general notion of "what is a cell" and can identify them across different domains of cellular imaging data have proven elusive. In this work, we present CellSAM, a foundation model for cell segmentation that generalizes across diverse cellular imaging data. CellSAM builds on top of the Segment Anything Model (SAM) by developing a prompt engineering approach for mask generation. We train an object detector, CellFinder, to automatically detect cells and prompt SAM to generate segmentations. We show that this approach allows a single model to achieve human-level performance for segmenting images of mammalian cells (in tissues and cell culture), yeast, and bacteria collected across various imaging modalities. We show that CellSAM has strong zero-shot performance and can be improved with a few examples via few-shot learning. We also show that CellSAM can unify bioimaging analysis workflows such as spatial transcriptomics and cell tracking. A deployed version of CellSAM is available at https://cellsam.deepcell.org/.

Optimal reward harvesting in complex perceptual environments.

The ability to choose rapidly among multiple targets embedded in a complex perceptual environment is key to survival. Targets may differ in their reward value as well as in their low-level perceptual properties (e.g., visual saliency). Previous studies investigated separately the impact of either value or saliency on choice; thus, it is not known how the brain combines these two variables during decision making. We addressed this question with three experiments in which human subjects attempted to maximize their monetary earnings by rapidly choosing items from a brief display. Each display contained several worthless items (distractors) as well as two targets, whose value and saliency were varied systematically. We compared the behavioral data with the predictions of three computational models assuming that (i) subjects seek the most valuable item in the display, (ii) subjects seek the most easily detectable item, and (iii) subjects behave as an ideal Bayesian observer who combines both factors to maximize the expected reward within each trial. Regardless of the type of motor response used to express the choices, we find that decisions are influenced by both value and feature-contrast in a way that is consistent with the ideal Bayesian observer, even when the targets' feature-contrast is varied unpredictably between trials. This suggests that individuals are able to harvest rewards optimally and dynamically under time pressure while seeking multiple targets embedded in perceptual clutter.

Anatomically distributed neural representations of instincts in the hypothalamus.

Artificial activation of anatomically localized, genetically defined hypothalamic neuron populations is known to trigger distinct innate behaviors, suggesting a hypothalamic nucleus-centered organization of behavior control. To assess whether the encoding of behavior is similarly anatomically confined, we performed simultaneous neuron recordings across twenty hypothalamic regions in freely moving animals. Here we show that distinct but anatomically distributed neuron ensembles encode the social and fear behavior classes, primarily through mixed selectivity. While behavior class-encoding ensembles were spatially distributed, individual ensembles exhibited strong localization bias. Encoding models identified that behavior actions, but not motion-related variables, explained a large fraction of hypothalamic neuron activity variance. These results identify unexpected complexity in the hypothalamic encoding of instincts and provide a foundation for understanding the role of distributed neural representations in the expression of behaviors driven by hardwired circuits.

Automated monitoring and analysis of social behavior in Drosophila.

We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship 'song') and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression.

High-throughput ethomics in large groups of Drosophila.

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

Self-Supervised Keypoint Discovery in Behavioral Videos.

We propose a method for learning the posture and structure of agents from unlabelled behavioral videos. Starting from the observation that behaving agents are generally the main sources of movement in behavioral videos, our method, Behavioral Keypoint Discovery (B-KinD), uses an encoder-decoder architecture with a geometric bottleneck to reconstruct the spatiotemporal difference between video frames. By focusing only on regions of movement, our approach works directly on input videos without requiring manual annotations. Experiments on a variety of agent types (mouse, fly, human, jellyfish, and trees) demonstrate the generality of our approach and reveal that our discovered keypoints represent semantically meaningful body parts, which achieve state-of-the-art performance on keypoint regression among self-supervised methods. Additionally, B-KinD achieve comparable performance to supervised keypoints on downstream tasks, such as behavior classification, suggesting that our method can dramatically reduce model training costs vis-a-vis supervised methods.

Measuring and Predicting Object Importance.

How important is a particular object in a photograph of a complex scene? We propose a definition of importance and present two methods for measuring object importance from human observers. Using this ground truth, we fit a function for predicting the importance of each object directly from a segmented image; our function combines a large number of object-related and image-related features. We validate our importance predictions on 2,841 objects and find that the most important objects may be identified automatically. We find that object position and size are particularly informative, while a popular measure of saliency is not.

A common genetic target for environmental and heritable influences on aggressiveness in Drosophila.

Environmental and genetic factors can modulate aggressiveness, but the biological mechanisms underlying their influence are largely unknown. Social experience with conspecifics suppresses aggressiveness in both vertebrate and invertebrate species, including Drosophila. We searched for genes whose expression levels correlate with the influence of social experience on aggressiveness in Drosophila by performing microarray analysis of head tissue from socially isolated (aggressive) vs. socially experienced (nonaggressive) male flies. Among approximately 200 differentially expressed genes, only one was also present in a gene set previously identified by profiling Drosophila strains subjected to genetic selection for differences in aggressiveness [Dierick HA, Greenspan RJ (2006) Nat Genet 38:1023-1031]. This gene, Cyp6a20, encodes a cytochrome P450. Social experience increased Cyp6a20 expression and decreased aggressiveness in a reversible manner. In Cyp6a20 mutants, aggressiveness was increased in group-housed but not socially isolated flies. These data identify a common genetic target for environmental and heritable influences on aggressiveness. Cyp6a20 is expressed in a subset of nonneuronal support cells associated with pheromone-sensing olfactory sensilla, suggesting that social experience may influence aggressiveness by regulating pheromone sensitivity.

Mice in a labyrinth show rapid learning, sudden insight, and efficient exploration.

Animals learn certain complex tasks remarkably fast, sometimes after a single experience. What behavioral algorithms support this efficiency? Many contemporary studies based on two-alternative-forced-choice (2AFC) tasks observe only slow or incomplete learning. As an alternative, we study the unconstrained behavior of mice in a complex labyrinth and measure the dynamics of learning and the behaviors that enable it. A mouse in the labyrinth makes ~2000 navigation decisions per hour. The animal explores the maze, quickly discovers the location of a reward, and executes correct 10-bit choices after only 10 reward experiences - a learning rate 1000-fold higher than in 2AFC experiments. Many mice improve discontinuously from one minute to the next, suggesting moments of sudden insight about the structure of the labyrinth. The underlying search algorithm does not require a global memory of places visited and is largely explained by purely local turning rules.

Task Programming: Learning Data Efficient Behavior Representations.

Specialized domain knowledge is often necessary to accurately annotate training sets for in-depth analysis, but can be burdensome and time-consuming to acquire from domain experts. This issue arises prominently in automated behavior analysis, in which agent movements or actions of interest are detected from video tracking data. To reduce annotation effort, we present TREBA: a method to learn annotation-sample efficient trajectory embedding for behavior analysis, based on multi-task self-supervised learning. The tasks in our method can be efficiently engineered by domain experts through a process we call "task programming", which uses programs to explicitly encode structured knowledge from domain experts. Total domain expert effort can be reduced by exchanging data annotation time for the construction of a small number of programmed tasks. We evaluate this trade-off using data from behavioral neuroscience, in which specialized domain knowledge is used to identify behaviors. We present experimental results in three datasets across two domains: mice and fruit flies. Using embeddings from TREBA, we reduce annotation burden by up to a factor of 10 without compromising accuracy compared to state-of-the-art features. Our results thus suggest that task programming and self-supervision can be an effective way to reduce annotation effort for domain experts.

The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice.

The study of naturalistic social behavior requires quantification of animals' interactions. This is generally done through manual annotation-a highly time-consuming and tedious process. Recent advances in computer vision enable tracking the pose (posture) of freely behaving animals. However, automatically and accurately classifying complex social behaviors remains technically challenging. We introduce the Mouse Action Recognition System (MARS), an automated pipeline for pose estimation and behavior quantification in pairs of freely interacting mice. We compare MARS's annotations to human annotations and find that MARS's pose estimation and behavior classification achieve human-level performance. We also release the pose and annotation datasets used to train MARS to serve as community benchmarks and resources. Finally, we introduce the Behavior Ensemble and Neural Trajectory Observatory (BENTO), a graphical user interface for analysis of multimodal neuroscience datasets. Together, MARS and BENTO provide an end-to-end pipeline for behavior data extraction and analysis in a package that is user-friendly and easily modifiable.