A Comparison between Mouse, In Silico, and Robot Odor Plume Navigation Reveals Advantages of Mouse Odor Tracking

The spiking output of the mouse olfactory bulb encodes large-scale temporal features of natural odor environments

In natural odor environments, odor travels in plumes. Odor concentration dynamics change in characteristic ways across the width and length of a plume. Thus, spatiotemporal dynamics of plumes have informative features for animals navigating to an odor source. Population activity in the olfactory bulb (OB) has been shown to follow odor concentration across plumes to a moderate degree (Lewis et al., 2021). However, it is unknown whether the ability to follow plume dynamics is driven by individual cells or whether it emerges at the population level. Previous research has explored the responses of individual OB cells to isolated features of plumes, but it is difficult to adequately sample the full feature space of plumes as it is still undetermined which features navigating mice employ during olfactory guided search. Here we released odor from an upwind odor source and simultaneously recorded both odor concentration dynamics and cellular response dynamics in awake, head-fixed mice. We found that longer timescale features of odor concentration dynamics were encoded at both the cellular and population level. At the cellular level, responses were elicited at the beginning of the plume for each trial, signaling plume onset. Plumes with high odor concentration elicited responses at the end of the plume, signaling plume offset. Although cellular level tracking of plume dynamics was observed to be weak, we found that at the population level, OB activity distinguished whiffs and blanks (accurately detected odor presence versus absence) throughout the duration of a plume. Even ∼20 OB cells were enough to accurately discern odor presence throughout a plume. Our findings indicate that the full range of odor concentration dynamics and high frequency fluctuations are not encoded by OB spiking activity. Instead, relatively lower-frequency temporal features of plumes, such as plume onset, plume offset, whiffs, and blanks, are represented in the OB.

Miniscope Recording Calcium Signals at Hippocampus of Mice Navigating an Odor Plume

Mice are able to navigate an odor plume with a complex spatiotemporal structure in the dark to find the source of odorants. We developed a protocol to monitor behavior and record Ca 2+ transients in dorsal CA1 stratum pyramidale neurons at the hippocampus (dCA1) in mice navigating an odor plume in a 50 cm x 50 cm x 25 cm odor arena. Ca 2+ transients were imaged by an epifluorescence miniscope focused through a GRIN lens on dCA1 neurons expressing the calcium sensor GCaMP6f in Thy1-GCaMP6f mice. We describe the behavioral protocol to train the mice to perform this odor plume navigation task in an automated odor arena. We provide the step-by-step procedure for the surgery for GRIN lens implantation and baseplate placement for imaging GCaMP6f in CA1. We provide information on real time tracking of the mouse position to automate the start of the trials and delivery of a sugar water reward. In addition, we provide information on the use of an Intan board to synchronize metadata describing the automation of the odor navigation task and frame times for the miniscope and a FLIR camera tracking mouse position. Moreover, we delineate the pipeline used to process GCaMP6f fluorescence movies by motion correction using NorMCorre followed by identification of regions of interest (ROIs) with EXTRACT. Finally, we describe use of artificial neural network (ANN) machine learning to decode spatial paths from CA1 neural ensemble activity to predict mouse navigation of the odor plume.

SUMMARY

This protocol describes how to investigate the brain-behavior relationship in hippocampal CA1 in mice navigating an odor plume. We provide a step-by-step protocol including the surgery to access imaging of the hippocampus, behavioral training, miniscope GCaMP6f recording and processing of the brain and behavioral data to decode the mouse position from ROI neural activity.

Behavioral discrimination and olfactory bulb encoding of odor plume intermittency

In order to survive, animals often need to navigate a complex odor landscape where odors can exist in airborne plumes. Several odor plume properties change with distance from the odor source, providing potential navigational cues to searching animals. Here, we focus on odor intermittency, a temporal odor plume property that measures the fraction of time odor is above a threshold at a given point within the plume and decreases with increasing distance from the odor source. We sought to determine if mice can use changes in intermittency to locate an odor source. To do so, we trained mice on an intermittency discrimination task. We establish that mice can discriminate odor plume samples of low and high intermittency and that the neural responses in the olfactory bulb can account for task performance and support intermittency encoding. Modulation of sniffing, a behavioral parameter that is highly dynamic during odor-guided navigation, affects both behavioral outcome on the intermittency discrimination task and neural representation of intermittency. Together, this work demonstrates that intermittency is an odor plume property that can inform olfactory search and more broadly supports the notion that mammalian odor-based navigation can be guided by temporal odor plume properties.

Recruitment of grid-like responses in human entorhinal and piriform cortices by odor landmark-based navigation

Olfactory navigation is universal across the animal kingdom. Humans, however, have rarely been considered in this context. Here, we combined olfactometry techniques, virtual reality (VR) software, and neuroimaging methods to investigate whether humans can navigate an olfactory landscape by learning the spatial relationships among discrete odor cues and integrating this knowledge into a spatial map. Our data show that over time, participants improved their performance on the odor navigation task by taking more direct paths toward targets and completing more trials within a given time period. This suggests that humans can successfully navigate a complex odorous environment, reinforcing the notion of human olfactory navigation. fMRI data collected during the olfactory navigation task revealed the emergence of grid-like responses in entorhinal and piriform cortices that were attuned to the same grid orientation. This result implies the existence of a specialized olfactory grid network tasked with guiding spatial navigation based on odor landmarks.

A map of spatial navigation for neuroscience

Spatial navigation has received much attention from neuroscientists, leading to the identification of key brain areas and the discovery of numerous spatially selective cells. Despite this progress, our understanding of how the pieces fit together to drive behavior is generally lacking. We argue that this is partly caused by insufficient communication between behavioral and neuroscientific researchers. This has led the latter to under-appreciate the relevance and complexity of spatial behavior, and to focus too narrowly on characterizing neural representations of space-disconnected from the computations these representations are meant to enable. We therefore propose a taxonomy of navigation processes in mammals that can serve as a common framework for structuring and facilitating interdisciplinary research in the field. Using the taxonomy as a guide, we review behavioral and neural studies of spatial navigation. In doing so, we validate the taxonomy and showcase its usefulness in identifying potential issues with common experimental approaches, designing experiments that adequately target particular behaviors, correctly interpreting neural activity, and pointing to new avenues of research.

The Grossberg Code: Universal Neural Network Signatures of Perceptual Experience

Two universal functional principles of Grossberg’s Adaptive Resonance Theory decipher the brain code of all biological learning and adaptive intelligence. Low-level representations of multisensory stimuli in their immediate environmental context are formed on the basis of bottom-up activation and under the control of top-down matching rules that integrate high-level, long-term traces of contextual configuration. These universal coding principles lead to the establishment of lasting brain signatures of perceptual experience in all living species, from aplysiae to primates. They are re-visited in this concept paper on the basis of examples drawn from the original code and from some of the most recent related empirical findings on contextual modulation in the brain, highlighting the potential of Grossberg’s pioneering insights and groundbreaking theoretical work for intelligent solutions in the domain of developmental and cognitive robotics.

Odor encoding by signals in the olfactory bulb

To understand the operation of the olfactory system, it is essential to know how information is encoded in the olfactory bulb. We applied Shannon information theoretic methods to address this, with signals from up to 57 glomeruli simultaneously optically imaged from presynaptic inputs in glomeruli in the mouse dorsal (dOB) and lateral (lOB) olfactory bulb, in response to six exemplar pure chemical odors. We discovered that, first, the tuning of these signals from glomeruli to a set of odors is remarkably broad, with a mean sparseness of 0.83 and a mean signal correlation of 0.64. Second, both of these factors contribute to the low information that is available from the responses of even populations of many tens of glomeruli, which was only 1.35 bits across 33 glomeruli on average, compared with the 2.58 bits required to perfectly encode these six odors. Third, although there is considerable interest in the possibility of temporal encoding of stimulus including odor identity, the amount of information in the temporal aspects of the presynaptic glomerular responses was low (mean 0.11 bits) and, importantly, was redundant with respect to the information available from the rates. Fourth, the information from simultaneously recorded glomeruli asymptotes very gradually and nonlinearly, showing that glomeruli do not have independent responses. Fifth, the information from a population became available quite rapidly, within 100 ms of sniff onset, and the peak of the glomerular response was at 200 ms. Sixth, the information from the lOB was not additive with that of the dOB.NEW & NOTEWORTHY We report broad tuning and low odor information available across the lateral and dorsal bulb populations of glomeruli. Even though response latencies can be significantly predictive of stimulus identity, such contained very little information and none that was not redundant with information based on rate coding alone. Last, in line with the emerging notion of the important role of earliest stages of responses ("primacy"), we report a very rapid rise in information after each inhalation.

Using your nose to find your way: Ethological comparisons between human and non-human species

Olfaction is arguably the least valued among our sensory systems, and its significance for human behavior is often neglected. Spatial navigation represents no exception to the rule: humans are often characterized as purely visual navigators, a view that undermines the contribution of olfactory cues. Accordingly, research investigating whether and how humans use olfaction to navigate space is rare. In comparison, research on olfactory navigation in non-human species is abundant, and identifies behavioral strategies along with neural mechanisms characterizing the use of olfactory cues during spatial tasks. Using an ethological approach, our review draws from studies on olfactory navigation across species to describe the adaptation of strategies under the influence of selective pressure. Mammals interact with spatial environments by abstracting multisensory information into cognitive maps. We thus argue that olfactory cues, alongside inputs from other sensory modalities, play a crucial role in spatial navigation for mammalian species, including humans; that is, odors constitute one of the many building blocks in the formation of cognitive maps.

Principles of odor coding in vertebrates and artificial chemosensory systems

The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall I-O relationships. Up to this point, our account of the systems goes along similar lines. The next processing steps differ considerably: while in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers were little studied. Only recently there has been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little connected fields.

Plume Dynamics Structure the Spatiotemporal Activity of Mitral/Tufted Cell Networks in the Mouse Olfactory Bulb

Although mice locate resources using turbulent airborne odor plumes, the stochasticity and intermittency of fluctuating plumes create challenges for interpreting odor cues in natural environments. Population activity within the olfactory bulb (OB) is thought to process this complex spatial and temporal information, but how plume dynamics impact odor representation in this early stage of the mouse olfactory system is unknown. Limitations in odor detection technology have made it difficult to measure plume fluctuations while simultaneously recording from the mouse's brain. Thus, previous studies have measured OB activity following controlled odor pulses of varying profiles or frequencies, but this approach only captures a subset of features found within olfactory plumes. Adequately sampling this feature space is difficult given a lack of knowledge regarding which features the brain extracts during exposure to natural olfactory scenes. Here we measured OB responses to naturally fluctuating odor plumes using a miniature, adapted odor sensor combined with wide-field GCaMP6f signaling from the dendrites of mitral and tufted (MT) cells imaged in olfactory glomeruli of head-fixed mice. We precisely tracked plume dynamics and imaged glomerular responses to this fluctuating input, while varying flow conditions across a range of ethologically-relevant values. We found that a consistent portion of MT activity in glomeruli follows odor concentration dynamics, and the strongest responding glomeruli are the best at following fluctuations within odor plumes. Further, the reliability and average response magnitude of glomerular populations of MT cells are affected by the flow condition in which the animal samples the plume, with the fidelity of plume following by MT cells increasing in conditions of higher flow velocity where odor dynamics result in intermittent whiffs of stronger concentration. Thus, the flow environment in which an animal encounters an odor has a large-scale impact on the temporal representation of an odor plume in the OB. Additionally, across flow conditions odor dynamics are a major driver of activity in many glomerular networks. Taken together, these data demonstrate that plume dynamics structure olfactory representations in the first stage of odor processing in the mouse olfactory system.

Using Head-Mounted Ethanol Sensors to Monitor Olfactory Information and Determine Behavioral Changes Associated with Ethanol-Plume Contact during Mouse Odor-Guided Navigation

Olfaction guides navigation and decision-making in organisms from multiple animal phyla. Understanding how animals use olfactory cues to guide navigation is a complicated problem for two main reasons. First, the sensory cues used to guide animals to the source of an odor consist of volatile molecules, which form plumes. These plumes are governed by turbulent air currents, resulting in an intermittent and spatiotemporally varying olfactory signal. A second problem is that the technologies for chemical quantification are cumbersome and cannot be used to detect what the freely moving animal senses in real time. Understanding how the olfactory system guides this behavior requires knowing the sensory cues and the accompanying brain signals during navigation. Here, we present a method for real-time monitoring of olfactory information using low-cost, lightweight sensors that robustly detect common solvent molecules, like alcohols, and can be easily mounted on the heads of freely behaving mice engaged in odor-guided navigation. To establish the accuracy and temporal response properties of these sensors we compared their responses with those of a photoionization detector (PID) to precisely controlled ethanol stimuli. Ethanol-sensor recordings, deconvolved using a difference-of-exponentials kernel, showed robust correlations with the PID signal at behaviorally relevant time, frequency, and spatial scales. Additionally, calcium imaging of odor responses from the olfactory bulbs (OBs) of awake, head-fixed mice showed strong correlations with ethanol plume contacts detected by these sensors. Finally, freely behaving mice engaged in odor-guided navigation showed robust behavioral changes such as speed reduction that corresponded to ethanol plume contacts.

Spatial information from the odour environment in mammalian olfaction

The sense of smell is an essential modality for many species, in particular nocturnal and crepuscular mammals, to gather information about their environment. Olfactory cues provide information over a large range of distances, allowing behaviours ranging from simple detection and recognition of objects, to tracking trails and navigating using odour plumes from afar. In this review, we discuss the features of the natural olfactory environment and provide a brief overview of how odour information can be sampled and might be represented and processed by the mammalian olfactory system. Finally, we discuss recent behavioural approaches that address how mammals extract spatial information from the environment in three different contexts: odour trail tracking, odour plume tracking and, more general, olfactory-guided navigation. Recent technological developments have seen the spatiotemporal aspect of mammalian olfaction gain significant attention, and we discuss both the promising aspects of rapidly developing paradigms and stimulus control technologies as well as their limitations. We conclude that, while still in its beginnings, research on the odour environment offers an entry point into understanding the mechanisms how mammals extract information about space.