Biology subjects

Margrie, T. W.

Publications and source records attributed to Margrie, T. W..

12 recordsLinked to original sources

bioRxiv2026

High-throughput serial two-photon tomography with BakingTray and BrainSaw

Volumetric imaging is increasingly important in fields such as neuroscience, where quantifying structure and mapping features are inherently three-dimensional problems. Block-face serial two-photon tomography (STPT) has emerged as a powerful approach for high-resolution, whole-organ volumetric imaging. STPT avoids complex sample preparation and balances image quality, speed, and scalability. However, STPT remains niche, in part because of the absence of flexible, general-purpose control software. Here we present BakingTray, an open-source software platform for STPT that extends ScanImage. BakingTrays modular framework accommodates diverse hardware configurations and allows users to build systems customised to their needs. Twelve such systems, which we call BrainSaws, have been constructed worldwide since 2016, with more under construction, and have so far contributed to 35 research papers. The three systems at the Sainsbury Wellcome Centre alone have acquired over 7,000 samples in a busy multi-user facility. We demonstrate the platform across its core neuroscience applications: electrode track localisation, brain-wide cell counting, and bulk projection mapping. Beyond these, we map the cell-type-specific synaptic output of inhibitory neurons in the ventral lateral geniculate nucleus and, with whole-mount staining, amyloid plaques brain-wide in a mouse model of Alzheimers disease. BakingTray is a mature platform for groups or facilities needing a customised volumetric imaging solution, whether built new or converted cheaply from an existing two-photon microscope.

neuroscience↗

bioRxiv2025

Mapping the magnetoreceptive brain: A 3D digital atlas of the migratory bird Eurasian blackcap (Sylvia atricapilla)

Birds undisputedly range amongst natures foremost navigators. To successfully navigate between breeding and wintering quarters, they, in addition to other natural orientation cues, rely on their ability to sense the Earths magnetic field. For this reason, migratory birds have become key model species for studying the sensory mechanisms underlying magnetic field-guided navigation, as evidenced by the identification of several brain regions believed to be involved in processing magnetic field information. However, there is as yet no readily accessible, high-resolution three-dimensional (3D) brain atlas to serve as a common reference within and across studies. Here we provide the neuroscience research community with the first freely available, digital, high-resolution (25 {micro}m), 3D bird brain atlas. It is based on light microscopy images from ten Eurasian blackcaps (Sylvia atricapilla), a night-migratory songbird widely used model species in magnetoreception and navigation research. We outline the individual steps for the creation of a brain atlas, from whole-brain imaging using serial-section, two-photon tomography, to the creation of an average template at an isotropic 25-{micro}m voxel size, and finally to brain area segmentation and annotation. In this first version of the atlas, we have mapped a total of 24 brain areas, including 6 principal compartments, 13 conspicuous anatomical subdivisions common to all bird species and 5 functionally defined areas of the visual and trigeminal sensory systems involved in processing magnetic field information. This atlas is accessible via the standardised BrainGlobe Atlas API, making it compatible with a growing suite of computational neuroanatomy tools provided by the BrainGlobe Initiative. This integration enables precise alignment of future experimental data to a common coordinate space, facilitating collaboration, data visualization and sharing. Furthermore, this resource enables the accurate localization and comparison of implanted devices, injection sites, and/or cell populations across individual brains, both within and across studies.

neuroscience↗

bioRxiv2024

Overcoming off-target optical stimulation-evoked cortical activity in the mouse brain in vivo

Genetic engineering of exogenous opsins sensitive to a wide range of lightwavelengths allows the interrogation of brain circuits to an unprecedented temporal and spatial precision. In particular, red-shifted opsins offer access deeper within the brain tissue. It is however crucial to consider the potential unintended back-activation of endogenous opsins due to laser light striking the back of the retina. Here, we found that in complete darkness and with no expression of exogenous opsins, optical fiber laser stimulation at wavelengths of 637 nm (red), 594 nm (orange), or 473 nm (blue) from within the ipsilateral mouse visual cortex resulted in a strong neuronal response in its contralateral counterpart. This neuronal activation occurred even at low laser intensities (1mW at the fiber tip, 31.8mW/mm2) and was most pronounced using red wavelengths. We therefore took advantage of retinal light adaptation using external illumination with a relatively dim ambient light source (20 lux) which was found to completely abolish orange and blue laser-evoked neuronal activation from within the brain, even at high laser intensities (15mW, 477.3mW/mm2). To prevent red laser-evoked retinal activation, however, only much lower intensities (2.5mW, 79.6mW/mm2) combined with external illumination (20 lux) could be used. These findings demonstrate the critical need for careful selection of light wavelengths and intensities for laser stimulation during optogenetic experiments in the mouse brain in vivo. Additionally, light adaptation of the retina through ambient light exposure offers an effective solution to minimize unintended retinal activation.

neuroscience↗

bioRxiv2024

Movie reconstruction from mouse visual cortex activity

The ability to reconstruct images represented by the brain has the potential to give us an intuitive understanding of what the brain sees. Reconstruction of visual input from human fMRI data has garnered significant attention in recent years. Comparatively less focus has been directed towards vision reconstruction from single-cell recordings, despite its potential to provide a more direct measure of the information represented by the brain. Here, we achieve high-quality reconstructions of natural movies presented to mice, from the activity of neurons in their visual cortex for the first time. Using our method of video optimization via backpropagation through a state-of-the-art dynamic neural encoding model we reliably reconstruct 10-second movies at 30 Hz from two-photon calcium imaging data. We achieve a pixel-level correction of 0.57 between the ground truth movie and the reconstructions from single-trial neural responses. We find that critical for high-quality reconstructions are the number of neurons in the dataset and the use of model ensembling. This paves the way for movie reconstruction to be used as a tool to investigate a variety of visual processing phenomena.

neuroscience↗

bioRxiv2024

Layer 6 corticocortical cells dominate the anatomical organization of intra and interhemispheric feedback

The mouse neocortex contains at least ninety distinctly defined yet interconnected areas that are symmetrically located across the two hemispheres. Determining the logic of this long range circuitry is necessary for understanding how inter-areal integration enables high level brain function involving multiple sensory, motor and cognitive processes. To address this we have performed a systematic anatomical analysis of the areal and laminar organization of the ipsilateral and contralateral cortical projection onto the primary visual (VISp), primary somatosensory barrel field (SSp-bfd) and primary motor (MOp) cortices. The resultant input maps reveal that although the ipsilateral hemisphere is the primary source of cortical input, there is substantial bilateral symmetry regarding the relative contribution and areal identity of contralateral input. Laminar analysis of these input areas show that excitatory Layer 6 corticocortical cells (L6 CCs) are a major projection pathway from both within and across the two hemispheres. Based on cortical hierarchy analysis that compares the relative contribution of inputs from supra-(feedforward) and infra-granular (feedback) layers, we find that contra-hemispheric projections reflect a dominant feedback organization compared to their ipsi-cortical counterpart. The magnitude of the interhemispheric difference in hierarchy was largest for sensory and motor projection areas compared to frontal, medial or lateral brain areas and can be explained by a proportional increase in input from L6 neurons. L6 CCs therefore not only mediate long-range cortical communication but also reflect its inherent feedback organization.

neuroscience↗

bioRxiv2023

Tonically active GABAergic neurons in the dorsal periaqueductal gray control the initiation and execution of instinctive escape

To avoid predation, animals perform defensive actions that are both instinctive and adaptable to the environment. In mice, the decision to escape from imminent threats is implemented by a feed-forward circuit in the midbrain, where excitatory VGluT2+ neurons in the dorsal periaqueductal gray (dPAG) compute escape initiation and escape vigour from threat evidence. Here we show that GABAergic VGAT+ neurons in the dPAG dynamically control this process by modulating the excitability of excitatory escape neurons. Using in vitro patchclamp and in vivo neural activity recordings in freely behaving mice we found that VGAT+ dPAG neurons fire action potentials tonically in the absence of synaptic inputs and are a major source of synaptic inhibition to VGluT2+ dPAG neurons. Activity in these spontaneously firing VGAT+ cells transiently decreases at escape onset and increases during escape, peaking at escape termination. Optogenetically increasing or decreasing VGAT+ dPAG activity bidirectionally changes the probability of escape when the stimulation is delivered at the time of threat onset, and the duration of escape when delivered after escape initiation. We conclude that the activity of tonically firing VGAT+ dPAG neurons sets a threshold for escape initiation and controls the execution of the flight locomotor action.

neuroscience↗

bioRxiv2022

A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration

Tactile sensation and vision are often both utilized for the exploration of objects that are within reach though it is not known whether or how these two distinct sensory systems might combine such information. Here in mice we find that stimulation of the contralateral whisker array suppresses visually evoked activity in a subarea of primary visual cortex (VISp) whose visual space covers the whisker search space. This is mediated by local fast spiking interneurons that receive a direct cortico-cortical input predominantly from layer 6 of the primary somatosensory barrel cortex (SSp-bfd). These data demonstrate functional convergence within and between two primary sensory cortical areas for multisensory object detection and recognition.

neuroscience↗

bioRxiv2021

Tools for accurate post hoc determination of marker location within whole-brain microscopy images

To interpret in vivo experiments designed to understand brain function, high-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and recorded cells in three dimensional brain space that is a critical step for data interrogation. Here we have developed Python-based tools (brainreg and brainreg-segment) to accurately map, in a common coordinate space, the position of dye-labelled probe tracks and two-photon imaged cell populations expressing fluorescent protein. The precise location of probes and cells were validated using physiological recordings and human raters that indicate accuracy levels to less than 70{micro}m. These flexible, open-source methodologies are expected to further evolve with need and to deliver the anatomical precision that is necessary for understanding the functional architecture of the brain.

neuroscience↗

bioRxiv2021

The retrosplenial cortex combines internal and external cues to encode head velocity during navigation

The extent to which we successfully navigate the environment depends on our ability to continuously track our heading direction and speed. Angular head velocity (AHV) cells, which encode the speed and direction of head turns during navigation, are fundamental to this process, yet the mechanisms that determine their function remain unknown. By performing chronic single-unit recordings in the retrosplenial cortex (RSP) of the mouse and tracking the activity of individual AHV neurons between freely moving and head-restrained conditions, we find that vestibular inputs dominate AHV signalling. In addition, we discover that self-generated optic flow input onto these neurons increases the gain and signal-to-noise ratio of angular velocity coding during free exploration. Psychophysical experiments and neural decoding further reveal that vestibular-visual integration increases the perceptual accuracy of egocentric angular velocity and the fidelity of its representation by RSP ensembles. We propose that while AHV coding is dependent on vestibular input, it also uses vision to maximise navigation accuracy in nocturnal and diurnal environments.

neuroscience↗

bioRxiv2020

A deep learning algorithm for 3D cell detection in whole mouse brain image datasets

Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. How-ever, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an opensource algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.

neuroscience↗

bioRxiv2020

Excitatory and inhibitory L2/3 neurons in mouse primary visual cortex are balanced in their input connectivity

Quantitatively characterising brain-wide connectivity of neural circuits is of vital importance in understanding the function of the mammalian cortex. Here we have designed an analytical approach to examine data from hierarchical segmentation ontologies, and applied it in the comparison of long-range presynaptic connectivity onto excitatory and inhibitory neurons in layer 2/3 (L2/3) of mouse primary visual cortex (V1). We find that long-range connections onto these two general cell classes in L2/3 originate from highly similar brain regions, and in similar proportions, when compared to input to layer 6. These anatomical data suggest that distal information received by excitatory and inhibitory networks is highly homogenous in L2/3.

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bioRxiv2018

Visual experience regulates the intrinsic excitability of visual cortical neurons to maintain sensory function

This in vivo study shows that both intrinsic and sensory-evoked synaptic properties of layer 2/3 neurons in mouse visual cortex are modified by ongoing visual input. Following visual deprivation, intrinsic properties are significantly altered, although orientation selectivity across the population remains unchanged. We therefore suggest that cortical cells adjust their intrinsic excitability in an activity-dependent manner to compensate for changes in synaptic drive and maintain sensory network function.

neuroscience↗