3 research outputs found
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A Neural Signal Processor for Low-Latency Spike Inference
This thesis describes the development of a system that can assign identities to a population of single-units, in multi-electrode recordings, at single-spike resolution with low-latency. The system has two parts. The first is a Field-Programmable Gate Array (FPGA)-based Neural Signal Processor (NSP) that receives raw input and generates labelled spikes as output, a process referred to as real-time spike inference. The second is a piece of software (Spiketag) that runs on a PC, communicates with the NSP, and generates a spike-sorted model to guide the real-time spike inference. The NSP provides clocks and control signals to five 32-channel INTAN RHD2132 chips to manage the acquisition of 160 channels of raw neural data. In parallel, the NSP further filters, detects and extracts extracellular spike waveforms from the raw neural data recorded by tetrodes or silicon probes and assigns single-unit identity to each detected spike. A set of Python application programming interfaces (APIs) was developed in Spiketag to enable the communication between the NSP and the PC. These APIs allow the NSP to obtain a model from the PC, which holds parameters such as reference channels, spike detection thresholds, spike feature transformation matrix and vector quantized clusters generated by spike sorting a short recording session. Using the spike-sorted model, the NSP performs data acquisition and real-time spike inference simultaneously. Algorithmic modules were implemented in the FPGA and pipelined to compute during 40 ms acquisition intervals. At the output end of the FPGA NSP, the real-time assigned single-unit identity (spike-id) is packaged with the timestamp, the electrode group, and the spike features as a spike-id packet. Spike-id packets are asynchronously transmitted through a low-latency Peripheral Component Interconnect Express (PCIe) interface to the PC, producing the real-time spike trains. The real-time spike trains can be used for further processing, such as real-time decoding. Several types of ground-truth data, including intracellular/extracellular paired recordings, synthesized
tetrode extracellular waveforms with ground-truth spike timing and high-channel-count silicon probe recordings with ground-truth animal positions during navigation were used to validate the low-latency (1 ms) and high-accuracy (as high as state-of-the-art offline sorting and decoding algorithms) of the NSPās real-time spike inference and the NSP-based
real-time population decoding performance
Volitional activation of remote place representations with a hippocampal braināmachine interface
Overview
This repository is associated with the following paper: Lai C, Tanaka S, Harris TD, Lee AK. Volitional activation of remote place representations with a hippocampal braināmachine interface. Science, 2023 (in press).
This dataset demonstrates the ability of animals to activate remote place representations within the hippocampus when they aren't physically present at those locations. Such remote activations serve as a fundamental capability underpinning memory recall, mental simulation/planning, imagination, and reasoning. By employing a hippocampal map-based brain-machine interface (BMI), we designed two specific tasks to test whether animals can intentionally control their hippocampal activity in a flexible, goal-directed, and model-based manner. Our results show that animals can perform both tasks in real-time and in single trials. This dataset provides the neural and behavior data of these two tasks. The details of the tasks and results are described in the paper.
Dataset, pre-trained model and code access:
Unzip the data.7z to get a data folder. The data folder contains three subfolders:
1. Running: This folder has two subfolders:
run_before_jumper: Contains data files for the Running task performed before the Jumper task.
run_before_jedi: Contains data files for the Running task performed before the Jedi task.
2. Jumper: Contains data files for the Jumper task.
2. Jedi: Contains data files for the Jedi task.
Unzip the model.7z to get a pretrained_model folder, which contains all 6 pretrained models (pth files) trained using the data from the Running tasks, 3 used in Jumper tasks and 3 used in the Jedi tasks.
Unzip the code.7