Biology subjects

Baden, T.

Publications and source records attributed to Baden, T..

28 records · Page 2Linked to original sources

bioRxiv2019

Divergent excitation two photon microscopy for 3D random access mesoscale imaging at single cell resolution

ABSTACTIn neuroscience, diffraction limited two-photon (2P) microscopy is a cornerstone technique that permits minimally invasive optical monitoring of neuronal activity. However, most conventional 2P microscopes impose significant constraints on the size of the imaging field-of-view and the specific shape of the effective excitation volume, thus limiting the scope of biological questions that can be addressed and the information obtainable. Here, employing divergent beam optics (DBO), we present an ultra-low-cost, easily implemented and flexible solution to address these limitations, offering a several-fold expanded three-dimensional field of view that also maintains single-cell resolution. We show that this implementation increases both the space-bandwidth product and effective excitation power, and allows for straight-forward tailoring of the point-spread-function. Moreover, rapid laser-focus control via an electrically tunable lens now allows near-simultaneous imaging of remote regions separated in three dimensions and permits the bending of imaging planes to follow natural curvatures in biological structures. Crucially, our core design is readily implemented (and reversed) within a matter of hours, and fully compatible with a wide range of existing 2P customizations, making it highly suitable as a base platform for further development. We demonstrate the application of our system for imaging neuronal activity in a variety of examples in mice, zebrafish and fruit flies.

neuroscience↗

bioRxiv2019

Type-specific dendritic integration in mouse retinal ganglion cells

Neural computation relies on the integration of synaptic inputs across a neurons dendritic arbour. However, the fundamental rules that govern dendritic integration are far from understood. In particular, it is still unclear how cell type-specific differences in dendritic integration arise from general features of neural morphology and membrane properties. Here, retinal ganglion cells (RGCs), which relay the visual systems first computations to the brain, represent an exquisite model. They are functionally and morphologically diverse yet defined, and they allow studying dendritic integration in a functionally relevant context. Here, we show how four morphologically distinct types of mouse RGC with shared excitatory synaptic input (transient Off alpha, transient Off mini, sustained Off, and F-miniOff) exhibit distinct dendritic integration rules. Using two-photon imaging of dendritic calcium signals and biophysical modelling, we demonstrate that these RGC types strongly differ in their spatio-temporal dendritic integration: In transient Off alpha cells, dendritic receptive fields displayed little spatial overlap, indicative of a dendritic arbour that is partitioned in largely isolated regions. In contrast, dendritic receptive fields in the other three RGCs overlapped greatly and were offset to the soma, suggesting strong synchronization of dendritic signals likely due to backpropagation of somatic signals. Also temporal correlation of dendritic signals varied extensively among these types, with transient Off mini cells displaying the highest correlation across their dendritic arbour. Modelling suggests that morphology alone cannot explain these differences in dendritic integration, but instead specific combinations of dendritic morphology and ion channel densities are required. Together, our results reveal how neurons exhibit distinct dendritic integration profiles tuned towards their type-specific computations in their circuits, with the interplay between morphology and ion channel complement as a key contributor.

neuroscience↗

bioRxiv2019

Cellular and molecular mechanisms of photoreceptor tuning for prey capture in larval zebrafish

In the eye, the function of same-type photoreceptors must be regionally adjusted to process a highly asymmetrical natural visual world. Here we show that UV-cones in the larval zebrafish area temporalis are specifically tuned for UV-bright prey capture in their upper frontal visual field, which uses the signal from a single cone at a time. For this, UV-detection efficiency is regionally boosted 42-fold. Next, in vivo 2-photon imaging, transcriptomics and computational modelling reveal that these cones use an elevated baseline of synaptic calcium to facilitate the encoding of bright objects, which in turn results from expressional tuning of phototransduction genes. Finally, this signal is further accentuated at the level of glutamate release driving retinal networks. These regional differences tally with variations between peripheral and foveal cones in primates and hint at a common mechanistic origin. Together, our results highlight a rich mechanistic toolkit for the tuning of neurons.

neuroscience↗

bioRxiv2019

An arbitrary-spectrum spatial visual stimulator for vision research

Visual neuroscientists require accurate control of visual stimulation. However, few stimulator solutions simultaneously offer high spatio-temporal resolution and free control over the spectra of the light sources, because they rely on off-the-shelf technology developed for human trichromatic vision. Importantly, consumer displays fail to drive UV-shifted short wavelength-sensitive photoreceptors, which strongly contribute to visual behaviour in many animals, including mice, zebrafish and fruit flies. Moreover, many non-mammalian species feature more than three spectral photoreceptor types. Here, we present a flexible, spatial visual stimulator with up to 6 arbitrary spectrum chromatic channels. It combines a standard digital light processing engine with open source hard- and software that can be easily adapted to the experimentalists needs. We demonstrate the capability of this general visual stimulator experimentally in the in vitro mouse retinal whole-mount and the in vivo zebrafish. Hereby, we intend starting a community effort of sharing and developing a common stimulator design.

neuroscience↗

bioRxiv2018

Spikeling: a low-cost hardware implementation of a spiking neuron for neuroscience teaching and outreach.

Understanding of how neurons encode and compute information is fundamental to our study of the brain, but opportunities for hands-on experience with neurophysiological techniques on live neurons are scarce in science education. Here, we present Spikeling, an open source {pound}25 in silico implementation of a spiking neuron that mimics a wide range of neuronal behaviours for classroom education and public neuroscience outreach. Spikeling is based on an Arduino microcontroller running the computationally efficient Izhikevich model of a spiking neuron. The microcontroller is connected to input ports that simulate synaptic excitation or inhibition, dials controlling current injection and noise levels, a photodiode that makes Spikeling light-sensitive and an LED and speaker that allows spikes to be seen and heard. Output ports provide access to variables such as membrane potential for recording in experiments or digital signals that can be used to excite other connected Spikelings. These features allow for the intuitive exploration of the function of neurons and networks. We also report our experience of using Spikeling as a teaching tool for undergraduate and graduate neuroscience education in Nigeria and the UK.

scientific communication and education↗

bioRxiv2018

A low-cost hyperspectral scanner for natural imaging above and under water

Hyperspectral imaging is a widely used technology for industrial and scientific purposes, but the high cost and large size of commercial setups have made them impractical for most basic research. Here, we designed and implemented a fully open source and low-cost hyperspectral scanner based on a commercial spectrometer coupled to custom optical, mechanical and electronic components. We demonstrate our scanners utility for natural imaging in both terrestrial and underwater environments. Our design provides sub-nm spectral resolution between 350-1000 nm, including the UV part of the light spectrum which has been mostly absent from commercial solutions and previous natural imaging studies. By comparing the full light spectra from natural scenes to the spectral sensitivity of animals, we show how our system can be used to identify subtle variations in chromatic details detectable by different species. In addition, we have created an open access database for hyperspectral datasets collected from natural scenes in the UK and India. Together with comprehensive online build- and use-instructions, our setup provides an inexpensive and customisable solution to gather and share hyperspectral imaging data.

neuroscience↗

bioRxiv2017

Zebrafish differentially process colour across visual space to match natural scenes

Animal eyes evolve to process behaviourally important visual information, but how retinas deal with statistical asymmetries in visual space remains poorly understood. Using hyperspectral imaging in the field, in-vivo 2-photon imaging of retinal neurons and anatomy, here we show that larval zebrafish use a highly anisotropic retina to asymmetrically survey their natural visual world. First, different neurons dominate different parts of the eye, and are linked to a systematic shift in inner retinal function: Above the animal, there is little colour in nature and retinal circuits are largely achromatic. Conversely, the lower visual field and horizon are colour-rich, and are predominately surveyed by chromatic and colour-opponent circuits that are spectrally matched to the dominant chromatic axes in nature. Second, above the frontal horizon, a high-gain ultraviolet-system piggy-backs onto retinal circuits, likely to support prey-capture. Our results demonstrate high functional diversity among single genetically and morphologically defined types of neurons.

neuroscience↗

bioRxiv2017

Local Signal Processing In Mouse Horizontal Cell Dendrites

The mouse retina contains a single type of horizontal cell, a GABAergic interneuron that samples from all cone photoreceptors within reach and modulates their glutamatergic output via parallel feedback mechanisms. Because horizontal cells form an electrically-coupled network, they have been implicated in global signal processing, such as large scale contrast enhancement. Recently, it has been proposed that horizontal cells can also act locally at the level of individual cone photoreceptors. To test this possibility physiologically, we used two-photon microscopy to record light stimulus-evoked Ca2+ signals in cone axon terminals and horizontal cell dendrites as well as glutamate release in the outer plexiform layer. By selectively stimulating the two mouse cone opsins with green and UV light, we assessed whether signals from individual cones remain \"isolated\" within horizontal cell dendritic tips, or whether they spread across the dendritic arbour. Consistent with the mouse s opsin expression gradient, we found that the Ca2+ signals recorded from dendrites of dorsal horizontal cells were dominated by M- and those of ventral horizontal cells by S-opsin activation. The signals measured in neighbouring horizontal cell dendritic tips varied markedly in their chromatic preference, arguing against global processing. Rather, our experimental data and results from biophysically realistic modelling support the idea that horizontal cells can process cone input locally, extending the \"classical\" view of horizontal cells function. Pharmacologically removing horizontal cells from the circuitry reduced the sensitivity of the cone signal to low frequencies, suggesting that local horizontal cell feedback shapes the temporal properties of cone output.\n\nHighlightsO_LILight-evoked Ca2+ signals in horizontal cell dendrites reflect opsin gradient\nC_LIO_LIChromatic preferences in neighbouring dendritic tips vary markedly\nC_LIO_LIMouse horizontal cells process cone photoreceptor input locally\nC_LIO_LILocal horizontal cell feedback shapes the temporal properties of cone output\nC_LI\n\neTOC BlurbChapot et al. show that local light responses in mouse horizontal cell dendrites inherit properties, including chromatic preference, from the presynaptic cone photoreceptor, suggesting that their dendrites can provide \"private\" feedback to cones, for instance, to shape the temporal filtering properties of the cone synapse.

neuroscience↗

bioRxiv2017

The 100 Euro Lab: A 3-D Printable Open Source Platform For Fluorescence Microscopy, Optogenetics And Accurate Temperature Control During Behaviour Of Zebrafish, Drosophila And C. elegans

SUMMARY SUMMARY INTRO RESULTS DISCUSSION CONCLUSION METHODS AUTHOR CONTRIBUTION SUPPLEMENTARY FIGURE 1 -... SUPPLEMENTARY TABLE 1 -... SUPPLEMENTARY ASSEMBLY AND USER... SUPPLEMENTARY VIDEOS REFERENCES Small, genetically tractable species such as larval zebrafish, Drosophila or C. elegans have become key model organisms in modern neuroscience. In addition to their low maintenance costs and easy sharing of strains across labs, one key appeal is the possibility to monitor single or groups of animals in a behavioural arena while controlling the activity of select neurons using optogenetic or thermogenetic tools. However, the purchase of a commercial solution for these types of ...

neuroscience↗

bioRxiv2016

Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes.

The ability to reliably and precisely deliver picolitre volumes is an important component of biological research. Here we describe a high-performance, low-cost, open hardware pressure ejection system (Openspritzer), which can be constructed from off the shelf components. When connected to a standard micro-pipette via suitable pneumatic tubing, the device is capable of delivering minute doses of reagents to a wide range of biological and chemical systems. In this work, we characterise the performance of the device and compare it to a popular commercial system using two-photon fluorescence microscopy. We found that Openspritzer provides the same level of control over delivered reagent dose as the commercial system. Next, we demonstrate the utility of Openspritzer in a series of standard neurobiological applications. First, we used Openspritzer to deliver precise amounts of the neurotransmitters glutamate and GABA to hippocampal neurons to elicit time- and dose-precise excitatory and inhibitory responses, respectively. Second, we used Openspritzer to deliver infectious viral and bacterial agents to living tissue. Viral transfection of hippocampal interneurons with channelrhodopsin allowed for the optogenetic manipulation of hippocampal circuitry with light. Finally, we successfully used Openspritzer to infect organotypic hippocampal slice cultures with fluorescent Mycobacterium bovis bacilli. We anticipate that due to its high performance and low cost Openspritzer will be of interest to a broad range of researchers working in the life and physical sciences.

neuroscience↗