Section
Seyed Yahya Shirazi
- Apr 2026
From 1,052 to 8,563: How AI Coding Agents Transformed My Research Workflows
1,052 GitHub contributions in 2024. 8,563 in the last year. This post covers how AI coding agents transformed my research workflows, the open-source plugins I built along the way, and a 10-week course to help the …

- Apr 2026
Blog
Personal and Professional Experiences
This section is dedicated to my personal and professional experiences that I don’t want to forget and might be worth sharing. The blogs span from technical details on using …
- Dec 2025
Image Annotation Tool: VLM-Based Annotation for Neuroscience
An annotation bank for the NSD Shared 1000 images generated using open-source Vision Language Models. The tool supports batch processing across multiple VLMs with plans to integrate Hierarchical Event Descriptors (HED) …

- Dec 2025
Data
Useful and public datasets
I list some datasets that I find useful and public here. Unless otherwise noted, all datasets are available for download from the NEMAR Archive
- Dec 2025
Annotation Garden Initiative: Collaborative Annotation for Neuroscience
AGI addresses the critical gap between increasingly complex naturalistic stimuli and the need for standardized, reusable annotations. Through GitHub-based version control and modern web interfaces, AGI enables …

- Sep 2025
Papers
- Sep 2025
Age-related Reorganization of Corticomuscular Connectivity During Locomotor Perturbations
How does the brain communicate with muscles during unexpected perturbations, and how does this change with age? We investigated corticomuscular connectivity during perturbed recumbent stepping in young and older adults …

- Sep 2025
The Lab Streaming Layer for Synchronized Multimodal Recording
The Lab Streaming Layer (LSL) presents a software-based solution for synchronizing data streams across multiple instruments in neurophysiological research. Utilizing per-sample time stamps and LAN-based time …

- Sep 2025
Signal Processing for Wearable Biosensors: Fundamentals and Techniques for Ring-Based Devices
Explore the theoretical foundations and practical implementation of signal processing techniques for ring-based wearable biosensors. This guide covers digital filter theory, z-transforms, real-time processing …
- Aug 2025
Health-Specific Evaluation for AI Systems
Learn how to evaluate AI systems in healthcare using specialized metrics and frameworks that address clinical validity, FDA regulatory requirements, bias detection, safety assessment, and practical implementation …
- Aug 2025
Statistical Analysis for Evaluation
Learn how to apply statistical methods for robust evaluation of models, including power analysis, mixed-effects models, bootstrap confidence intervals, multiple comparison corrections, and effect size calculations. This …
- Aug 2025
LLM Evaluation Methods
Learn about various methods for evaluating large language models (LLMs), including automatic metrics like BLEU and ROUGE, the LLM-as-judge paradigm, human-in-the-loop strategies, and specialized approaches for …
- Aug 2025
Human Evaluation & Psychometrics for AI Systems
This post provides a detailed overview of human evaluation and psychometrics in the context of AI systems, covering key concepts, reliability metrics, scale design, and practical implementation strategies. It includes …
- Aug 2025
NEMAR Dataset Citations Analysis Dashboard
This dashboard provides comprehensive analysis of dataset citations within the NEMAR ecosystem, revealing collaboration patterns, research trends, and the impact of open neuroscience data sharing on the research …

- Jul 2025
HBN Dataset Insights Dashboard
This is a data visualization dashboard for exploring the Healthy Brain Network EEG dataset. Features age and sex distributions, task availability metrics, mental health correlations, and per-release analysis across 11 …

- Jul 2025
Creating Interactive Dashboards in Hugo: A Complete Guide
Learn how to transform your Hugo static site into an interactive dashboard powerhouse using Chart.js, structured JSON data, and modern web development practices.
- Jun 2025
Adding Mermaid Diagrams to Hugo: From Partials to Production
Learn how to seamlessly integrate Mermaid diagram functionality into your Hugo website using partials, enabling beautiful flowcharts, sequences, and technical diagrams directly in markdown.
- Jun 2025
Simulating Scalp EEG from Ultrahigh-Density ECoG Data Illustrates Cortex to Scalp Projection Patterns
Using 1024-electrode ultrahigh-density electrocorticography (μECoG) data as ground truth, this study demonstrates that cortical activity from a small 3×3 cm patch projects broadly across the entire scalp surface, not …

- May 2025
Python's venv: A Comparison with Conda for Research Computing
This post explores Python’s built-in venv module, highlighting its advantages for research computing while comparing it with Conda to help researchers choose the right tool for their workflows.
- Jan 2025
Setting Up and Managing Git-Annex with Backblaze B2 Storage
This guide walks you through setting up git-annex with Backblaze B2 as remote storage, and covers common usage scenarios for managing large files in git repositories.
- Dec 2024
A Standardized Framework for Sensor Placement in Human Motion Capture and Wearable Applications
We present a comprehensive framework that standardizes sensor placement in human movement and physiological monitoring applications. Through precise definitions of anatomical landmarks, coordinate systems, and placement …

- Oct 2024
HBN-EEG: The FAIR implementation of the Healthy Brain Network (HBN) electroencephalography dataset
The HBN-EEG dataset provides a comprehensive collection of high-density EEG recordings from the Healthy Brain Network project, formatted in the Brain Imaging Data Structure (BIDS) standard. This dataset includes …

- Oct 2024
HBN-EEG: Healthy Brain Network EEG Datasets
The Healthy Brain Network EEG Datasets (HBN-EEG) includes 11 dataset releases containing EEG, behavioral data, and rich event annotations from participants aged 5-21 years, supporting large-scale analyses and …

- May 2024
Older adults use fewer muscles to overcome perturbations during a seated locomotor task
Older adults often demonstrate greater co-contraction and motor errors than young adults in response to motor perturbations. We demonstrated that older adults reduced their motor errors more than young adults with brief …

- Aug 2023
System and methods for biosignal detection and active noise cancellation
We developed a novel EEG system with a dual-electrode net structure for noise reduction and precise biosignal capture. Incorporating advanced software for signal processing, this invention enhances EEG accuracy, reduces …

- Jan 2023
Non-Parametric Functional Muscle Network as a Robust Biomarker of Fatigue
We show that the effects of fatigue on muscle coordination and neural drive can be reliably characterized using a non-parametric functional muscle network. The network demonstrated a consistent decrease in connectivity …

- Jan 2023
Re-Referencing Methods for High-Density EEG
This project investigates different re-referencing approaches for high-density EEG recordings, evaluating their effectiveness in reducing artifacts and improving source localization accuracy. The work contributes to best …

- Jul 2022
Nonlinear functional muscle network based on information theory tracks sensorimotor integration post stroke
We show that InfoMuNet, a novel functional biomarker based on a nonlinear network graph of muscle connectivity, can quantify the role of sensory information on motor performance. We demonstrate its potential use in …

- May 2022
Perilaryngeal-Cranial Functional Muscle Network Differentiates Vocal Tasks: A Multi-Channel sEMG Approach
We explored the potential of a functional muscle network to differentiate vocal tasks. The network robustly differentiated vocal tasks, while classic muscle activation assessment failed to differentiate. The study also …

- Mar 2021
Sensory feedback and assistive motor control for desk cycling
This project explores how sensory feedback can enhance motor control during desk cycling, with applications in rehabilitation and workplace wellness. The research focuses on optimizing user experience and therapeutic …

- Feb 2021
Differential Theta-Band Signatures of the Anterior Cingulate and Motor Cortices During Seated Locomotor Perturbations
We demonstrate that seated locomotor perturbations produce differential theta-band responses in the anterior cingulate and supplementary motor areas, suggesting that tuning perturbation parameters can potentially modify …

- Nov 2019
More Reliable EEG Electrode Digitizing Methods Can Reduce Source Estimation Uncertainty, but Current Methods Already Accurately Identify Brodmann Areas
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Abstract
Electroencephalography (EEG) and source estimation can be used to identify brain areas activated during a task, which could offer greater insight on cortical dynamics. Source …

- Mar 2019
Influence of Mismarking Fiducial Locations on EEG Source Estimation
Mismarking fiducial locations can systematically change EEG source locations. We inestigated this effect by systematically moving the fiducial locations to simulate such errors.
