Biology subjects

Koert, E.

Publications and source records attributed to Koert, E..

5 recordsLinked to original sources

bioRxiv2026

Multichannel optical cochlear implants enable spectrally distinct auditory activity

When hearing fails, cochlear implants (CIs) restore auditory perception. Yet, coding of spectral information remains a bottleneck because each electrode broadly activates the auditory nerve. As light can be more conveniently confined, optical (o)CIs present an alternative. Here, we combined expression of the potent channelrhodopsin ChReef in spiral ganglion neurons (SGNs) with oCIs comprising 5-10 green LEDs in gerbils. This combination enabled systematic comparison of encoding intensity and spectral information by individual oCI channels to acoustic and electrical stimulation within a translationally feasible energy range. Recordings from the inferior colliculus (ICC) showed that ChReef aligned SGN light sensitivity with LED radiant fluxes: ICC activity had thresholds <200 nJ and reached a maximum equivalent to that achieved with 51 dB SPL pure tones. Multichannel oCIs enabled tonotopically ordered, spectrally distinct stimulation that more closely resembled acoustic stimulation than did electrical stimulation. Some LEDs elicited multiple spectral peaks at higher intensities. Linear discriminant analysis of ICC activity indicated improved channel discriminability for optical over electrical stimulation. In summary, ,micro-joule oCI-stimulation achieves improved spectral resolution over state-of-the-art electrical stimulation.

neuroscience↗

bioRxiv2026

Optogenetic cochlear stimulation evokes midbrain activity with near-physiological temporal fidelity

When hearing fails, stimulation of the auditory nerve by electrical cochlear implants (eCIs) partially restores hearing, with most eCI users achieving open speech understanding. However, the broad current spread from each electrode limits frequency coding and speech understanding in daily situations with background noise. Spatially confined optogenetic stimulation by future optical cochlear implants (oCIs) improves frequency coding but millisecond closing kinetics of channelrhodopsins (ChRs) might limit temporal coding. Here, we evaluated the utility of fast-closing f-Chrimson for processing temporal information in the auditory system of Mongolian gerbils. We recorded neural activity in the inferior colliculus evoked by f-Chrimson-mediated optogenetic stimulation of the cochlea. F-Chrimson enabled energy-efficient stimulation of the auditory pathway at rates [≥]150 Hz, outperforming the slower ChR variants CatCh (blue) and ChReef (green). Energy thresholds for activation of the auditory pathway were in the low {micro}J range, between ChReef (sub-{micro}J) and CatCh. Dynamic range and frequency selectivity were comparable to previous observations with CatCh and outperformed electrical stimulation. In conclusion, employing fast-gating ChRs harnesses improved spectral coding without degrading temporal coding. The Paper Explained ProblemElectrical cochlear implants (eCIs) partially restore speech comprehension in most of 1 million otherwise severely deaf people. However, most CI-users face challenges hearing in daily situations. Spectrally more selective stimulation of the auditory nerve by optical cochlear implants (oCIs) promises to overcome this limitation. However, the closing kinetics of channelrhodopsins (ChR) limit the temporal bandwidth of bionic sound coding. Improving the ChR properties and evaluating temporal coding remain major objectives for developing hearing restoration by oCI. ResultsHere, we evaluate the utility of waveguide-based oCI using the fast-closing ChR Chrimson (f-Chrimson) for encoding of temporal, spectral and intensity information by multi-electrode-array (MEA) recordings from the midbrain. We compare f-Chrimson-mediated bionic coding to acoustic coding as well as to previous data acquired with optogenetic stimulation using other ChRs and with electrical stimulation. F-Chrimson enabled energy-efficient stimulation of the auditory pathway at rates [≥]150 Hz, outperforming the slower ChR variants CatCh (blue) and ChReef (green). Intensity and frequency coding were comparable to previous observations with CatCh and outperformed electrical stimulation. ImpactThis study demonstrates near physiological temporal coding with the fast-closing ChR f-Chrimson, indicating that improved spectral coding by oCI is not traded off by poor temporal fidelity.

neuroscience↗

bioRxiv2025

CochleaNet: deep learning-based image analysis for cochlear connectomics and gene therapy

With the emergence of gene and optogenetic therapies targeting deafness, the comprehensive analysis of the molecular anatomy and physiology of the cochlea has become ever more important. Here, we introduce CochleaNet, a deep learning-based framework to analyze volumetric imaging data obtained by light-sheet microscopy of decalcified, cleared and fluorescently labeled cochleae. CochleaNet covers the workflow from reconstruction of the cochlea to segmentation of inner hair cells, spiral ganglion neurons and their afferent synapses, to analyzing the expression of gene therapy products. We validated CochleaNet by comparison to manual image analysis. Trained on high isotropic resolution mouse data, CochleaNet was also applicable to the cochlea of the gerbil, another relevant animal model, and lower-resolution mouse data from a commercially available microscope. We conclude that the combination of light-sheet microscopy and image analysis with CochleaNet paves the way for rapid and reliable quantification of cochlear molecular anatomy and preclinical gene therapy outcomes.

neuroscience↗

bioRxiv2023

Combining biophysical models and machine learning to optimize implant geometry and stimulation protocol for intraneural electrodes

ObjectivePeripheral nerve interfaces have the potential to restore sensory, motor, and visceral functions. In particular, intraneural interfaces allow targeting deep neural structures with high selectivity, even if their performance strongly depends upon the implantation procedure and the subjects anatomy. Currently, few alternatives exist for the determination of the target subject structural and functional anatomy, and statistical characterizations from cadaveric samples are limited because of their high cost. We propose an optimization workflow that can guide both the pre-surgical planning and the determination of maximally selective multisite stimulation protocols for implants consisting of several intraneural electrodes, and we characterize its performance in silico. We show that the availability of structural and functional information leads to very high performances and allows taking informed decisions on neuroprosthetic design. ApproachWe employ hybrid models (HMs) of neuromodulation in conjunction with a machine learning-based surrogate model to determine fiber activation under electrical stimulation, and two steps of optimization through particle swarm optimization (PSO) to optimize in silico implant geometry, implantation and stimulation protocols using morphological data from the human median nerve at a reduced computational cost. Main resultsOur method allows establishing the optimal geometry of multi-electrode transverse intra-fascicular multichannel electrode (TIME) implants, the optimal number of electrodes to implant, their optimal insertion, and a set of multipolar stimulation protocols that lead in silico to selective activation of all the muscles innervated by the human median nerve. SignificanceWe show how to use effectively HMs for optimizing personalized neuroprostheses for motor function restoration. We provide in-silico evidences about the potential of multipolar stimulation to increase greatly selectivity. We also show that the knowledge of structural and functional anatomies of the target subject leads to very high selectivity and motivate the development of methods for their in vivo characterization.

bioengineering↗

bioRxiv2020

Small dendritic synapses enhance temporal coding in a model of cochlear nucleus bushy cells

Spherical bushy cells (SBC) in the the anteroventral cochlear nucleus can improve the temporal precision of the auditory nerve spiking activity despite receiving sometimes only a single suprathreshold axosomatic input. The interaction with small dendritic inputs could provide a possible explanation for this phenomenon. In a compartment model of spherical bushy cells with a stylized or realistic three-dimensional representation of the bushy dendrite we explored this proposal. Phase-locked dendritic inputs caused both a tonic depolarization and a modulation of the SBC membrane potential at the frequency of the stimulus but for plausible model parameters do not cause output action potentials (AP). The tonic depolarization increased the excitability of the SBC model. The modulation of the membrane potential caused a phase-dependent increase in the efficacy of the main axosomatic input to cause output AP. These effects increased the rate and the temporal precision of output AP. Rate was mainly increased for stimulus frequencies at and below the characteristic frequency of the main input. Precision mostly increased for higher frequencies above about 1 kHz. Dendritic morphological parameters, biophysical parameters of the dendrite and the synaptic inputs and tonotopic parameters of the inputs all affected the impact of dendritic synapses. This suggested the possibility of fine tuning of the effect the dendritic inputs have for different coding demands or input frequency ranges. Excitatory dendritic inputs modulate the processing of the main input and are thus a plausible mechanism for the improvement of temporal precision in spherical bushy cells.

neuroscience↗