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Kucukoglu, B.

Publications and source records attributed to Kucukoglu, B..

2 recordsLinked to original sources

Bayesian optimization of cortical neuroprosthetic vision using perceptual feedback

The challenge in cortical neuroprosthetic vision is determining the optimal, safe stimulation patterns for the visual cortex in order to evoke the desired perception in blind individuals--specifically, light perceptions known as phosphenes. Currently, clinical studies gain insights into the perceptual characteristics of the perceived phosphenes by asking for descriptions of provided stimulation protocols. However, the huge parameter space for multi-electrode stimulation settings makes it difficult to draw conclusions about the optimality of the stimulation patterns that lead to well-perceived phosphenes. A systematic search in the parameter space of the electrical stimulation is needed to achieve good perception. Bayesian optimization (BO) is a framework for finding optimal parameters efficiently. Using the patients scoring of the perception as feedback, a model of the patients response based on iteratively generated stimulation protocols can be built to maximize perception quality. A patient implanted with an intracortical 96-channel microelectrode array in their visual cortex was tested by iteratively presenting stimulation protocols, generated via BO for the first and random generation (RG) for the second experiment. Whereas standard BO methods do not scale well to problems with over a dozen inputs, we propose to optimize a set of 40 electrode currents using trust region-based BO. The generated protocols determine which electrodes are concurrently stimulated from the set and with how much current from a range of 0-50 {micro}A, on a maximum total current constraint of 500 {micro}A. The patient provided feedback for each stimulation based on their liking of the perception quality on a Likert scale, where a score of 7 indicated the highest quality and 0 no perception. In the BO experiment, the patient perception quality ratings gradually converged on higher values compared to the RG experiment. Similarly, gradually higher total current values were chosen by BO, in line with the observed preference of patients for higher currents due to brighter phosphenes. Finally, the electrodes that were observed to be more effective in producing phosphene perception in previous studies were gradually chosen more by BO also with the allocation of higher current values. This study demonstrates the power of BO in converging to optimal stimulation protocols based on patient feedback, providing a more efficient search for stimulation parameters for clinical studies.

bioengineering↗

Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution

Cryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography - a coherent diffractive imaging technique using 4D scanning transmission electron microscopy (4D-STEM) - has recently demonstrated excellent SNR and resolution down to tens of picometers for thin specimens imaged at room temperature. Here we applied 4D-STEM and ptychographic data analysis to frozen hydrated proteins, reaching sub-nanometer resolution 3D reconstructions. We employed low-dose cryo-EM with an aberration-corrected, convergent electron beam to collect 4D-STEM data for our reconstructions. The high frame rate of the electron detector allowed us to record large datasets of electron diffraction patterns with substantial overlaps between the interaction volumes of adjacent scan positions, from which the scattering potentials of the samples were iteratively reconstructed. The reconstructed micrographs show strong SNR enabling the reconstruction of the structure of apoferritin protein at up to 5.8 [A] resolution. We also show structural analysis of the Phi92 capsid and sheath, tobacco mosaic virus, and bacteriorhodopsin at slightly lower resolutions.

biophysics↗