Reproducibility of heart rate variability (HRV) analysis is limited by differences in preprocessing and computational conventions across software platforms. We developed HRV Studio, an open-source PyQt6-based desktop application integrating transparent HRV analysis with automated quality-control (QC) diagnostics. Validation included large-scale agreement with NeuroKit2, targeted Kubios benchmarking, spectral-method comparison, synthetic perturbation testing, recording-duration sensitivity analysis, and arrhythmia-focused QC stress testing. HRV Studio showed near-identical agreement for the widely used time-domain indices RMSSD and SDNN under matched conditions. In the primary five-minute NeuroKit2 comparison, frequency-domain median relative errors were 1.35% for LF, 0.18% for HF, and 1.41% for LF/HF, while VLF remained more convention-sensitive (37.79%). Nonlinear Poincaré indices also demonstrated high consistency. Sequence-harmonized Kubios benchmarking confirmed near-identical agreement for time-domain and nonlinear indices and strong agreement for most frequency-domain measures. Extended ten-minute analyses reproduced the same overall pattern with lower disagreement for some convention-sensitive spectral outputs. Synthetic and arrhythmia stress tests maintained 100% numerical stability while consistently triggering QC warnings. Overall, HRV Studio provides a transparent and reproducible platform for HRV research, with strong cross-platform consistency when NN sequences, preprocessing, and analytical conventions are harmonized. Stress-test results indicate computational robustness rather than clinical validation.
Transforming raw neuroimage archives into analysis-ready derivatives relies on three brittle stages: data standardization, modality-specific preprocessing, and quality control (QC). While individual neuroimaging tools are well developed, their orchestration requires project-specific scripts, environment-adaptive tuning, and labor-intensive manual QC. To address this, we introduce NeuroPilot, a multi-agent system that digitalizes the expertise of neuroimage processing, QC, and data management into three LLM-invocable skills: dcm2bids-skill, neuroimage-pre-skill, and qc-agent-skill. The LLM-driven agent autonomously orchestrates workflows, generalizing various infrastructure settings into a single configuration to achieve the highest scalability. Demonstrating the system's generalizability, we deployed NeuroPilot across 17 cohorts (>123,000 subjects) spanning infant to aging populations and multiple MRI modalities (structural, diffusion, functional). In practice, after standardizing data via the dcm2bids-skill, the agent dynamically routes datasets to the optimal neuroimage-pre-skill based on available modalities and cohort traits (e.g., dispatching T1w and fMRI data to fMRIPrep, or selecting specialized pipelines for infant cohorts). The qc-agent-skill then drives an evidence-based, semi-automated QC via a 3-D browser dashboard, utilizing a multi-tiered verification system to optimize failed cases and escalate complex issues for supervisor inspection. Quantitatively, our QC agent screened 558 production subjects, validating its automated flags against FreeSurfer's topology-defect metrics. The infant processing pipeline achieved a 100% (201/201) completion rate on QC-validated inputs. Importantly, NeuroPilot compresses the traditional 2--3 month timeline for training staff and processing complete datasets into a single week. NeuroPilot is deployed in https://wanda-cyberbench.com/.
Katy L. Scott, Sejin Kim, Joshua Siraj +6cs.CV cs.LG
Radiomics and imaging foundation models promise non-invasive biomarkers of tumour biology, yet predictive signatures may reflect tumour volume or acquisition artifacts rather than meaningful image structure. We introduce READII-2-ROQC, an open-source framework that uses volume-preserving negative controls to assess whether radiomic and deep imaging features capture independent spatial signals. READII-2-ROQC generates voxel-perturbed images across tumour, background and whole-image regions using configurable randomization strategies, then compares feature behaviour and model performance between original and control images. Applied to three public cancer imaging cohorts, the framework processed 3,552 tumour volumes and extracted PyRadiomics and foundation-model features from original images and nine matched controls. Reproducing published survival and HPV-status signatures, we show that multiple models retain performance after spatial structure is destroyed, revealing volume-driven or contextual confounding, whereas others show perturbation-sensitive signal. READII-2-ROQC provides a scalable quality-control strategy for developing interpretable, biologically grounded imaging biomarkers and reproducible radiomics workflows.
This tutorial paper provides a step-by-step, reproducible walkthrough of NeuraDock Agent, an open-source EEG agent focused on Alpha dynamics and visual cognitive-load analysis. The goal is practical: a reader should be able to install the agent, run EEG preprocessing and quality control, generate Alpha dynamics figures, perform within-subject Rest/Task visual cognitive-load comparison, run the public mini-dataset analyses and compare them with the reference validation summary, start an online dashboard, call the real-time API from an external application, and use the LLM interpretation layer to explain quality risks. Existing EEG toolkits provide excellent offline analysis, but assembling a real-time, quality-gated cognitive-load pipeline often requires manually bridging acquisition, custom QC, Alpha feature extraction, and a web API; this tutorial closes that offline-to-online gap. The tutorial uses a quality-gated workflow: downstream Alpha and workload metrics are computed only after preprocessing and QC gating rather than directly from raw EEG. In the included mini-dataset validation, the agent processed 18 recordings, generated 10 within-subject comparisons, observed task-related posterior Alpha suppression in 7 of 10 contrasts, estimated initial evidence of within-subject repeatability, and benchmarked local online API latency. The tutorial is intended for researchers, developers, and applied teams who want a transparent path from EEG files to real-time visual cognitive-load prototypes.