Projects |

PhD dissertation proposal

Tue, 07 Feb 2023 00:00:00 +0000

'Step the Brain along a Path' Lobby Installation

Fri, 09 Sep 2022 00:00:00 +0000

My advisor, Chris Rozell, has dedicated significant time and effort to engaging the public with the changes and challenges posed by nascent neurotechnology. These efforts came to fruition in a collaboration with the Terminus Modern Ballet Theatre to create a ballet performance that explores the brain and the challenges of brain-computer interfaces. The piece was called and was performed in the Ferst Center for the Arts at Georgia Tech in September 2022.

To enhance community engagement, I worked in a team with , , and to create a to accompany the performance. Our goal was to create an audiovisual presentation of data from the mouse hippocampus and those features relevant to everyday life and health. While Abigail provided data and Timothy composed the end music product, I created the visualizations and tried my hand at sonification—that is, the representation of data with sound. These audiovisual presentations were then incorporated into the larger installation (pictured above).

Sonification

I preprocessed the data to experiment with different signals that would be interesting to hear, for example:

Spikes for each place cell, sorted by location. I mapped these to notes of different scales and arpeggios in the hopes of hearing replay events. The data was too messy (and came from an Alzheimer’s disease model mouse) to hear the replays clearly, but it was an interesting exercise.
Sharp wave-ripple events
Theta and gamma oscillations, both the band-limited power and filtered signals

We created different tracks to represent different states of the mouse, using high/low theta power to determine “active”/“restful” states and ripples to define a “recall” state.

Videos

Continuous recording, 0.32x speed

High theta power segments, 0.17x speed

Low theta power segments, 0.31 speed

Sharp wave-ripple segments, 0.25x speed

The audio and video of the spikes are a bit out of sync on this video, unfortunately.

CLOCTools

Thu, 19 May 2022 00:00:00 +0000

A set of software to aid in real-time closed-loop optogenetic control. I have been involved in developing/maintaining ldsCtrlEst and supervising the development of lqmpc.

tklfp: Teleńczuk Kernel LFP

Wed, 12 Jan 2022 11:15:20 -0500

Cleo: Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed

Tue, 23 Nov 2021 17:22:21 -0500

A Python package built around Brian 2 designed as a testbed for bridging computational models and experiments for mesoscale neuroscience. Specifically, it allows for convenient simulation of closed-loop real-time stimulation, electrode recording, 2P imaging, and optogenetics with spiking network models and provides a modular interface to facilitate future additions.

MMAPPR2: Mutation Mapping from RNA Sequences

Mon, 12 Jul 2021 11:10:44 -0400

MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2 cross of forward genetic screens. It accepts aligned BAM files as well as a reference genome as input and identifies loci of high sequence disparity between the control and mutant RNA sequences. It is significantly faster than its predecessor ( ) and enhances its functionality by improving mutation localization and integrating with Ensembl’s Variant Effect Predictor, outputting a ranked list of candidate mutations.