bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.09.21.558786

Optimizing magnetometers arrays and pre-processing pipelines for multivariate pattern analysis

Bezsudnova, Y.·Jensen, O.
View original source ↗Export metadata ↓

Abstract

BackgroundMultivariate pattern analysis (MVPA) has proven an excellent tool in cognitive neuroscience used M/EEG, and MRI. It also holds a strong promise when applied to optically-pumped magnetometer-based magnetoencephalography. New methodTo optimize OPM-MEG systems for MVPA experiments this study examines data from a conventional MEG magnetometer array, focusing on appropriate noise reduction techniques for magnetometers. We also determined the least required number of sensors needed for robust MVPA for image categorization experiments. ResultsWe found that the use of signal space separation (SSS) significantly lowered the classification accuracy considering a sub-array of 102 magnetometers or a sub-array of 204 gradiometers. We also found that classification accuracy did not improve when going beyond 30 sensors irrespective of whether SSS has been applied. Comparison with existing methodsThe power spectra of data filtered with SSS has a substantially higher noise floor that data cleaned with SSP or HFC. Consequently, the MVPA decoding results obtained from the SSS-filtered data are significantly lower compared to all other methods employed. ConclusionsWhen designing an MEG system based on SQUID magnetometers optimized for multivariate analysis for image categorization experiments, about 30 magnetometers are sufficient. We advise against applying SSS filters to data from MEG and OPM systems prior to performing MVPA as this method, albeit reducing low-frequency external noise contributions, also introduces an increase in broadband noise. We recommend employing noise reduction techniques that either decrease or maintain the noise floor of the data like signal-space projection, homogeneous field correction and gradient noise reduction. HighlightsO_LIA sensor array of about 30 sensors is sufficient for multivariate pattern analysis using conventional MEG magnetometers for image classification. C_LIO_LIUsing signal space separation filter on magnetometer data prior to multivariate pattern analysis might reduce classification accuracy due to an increase in white noise in the data contributed by the algorithm. C_LIO_LIWhen performing multivariate data analysis, other noise reduction approaches that diminish the contribution of external noise sources and reduce the variance of the data are advisable such as synthetic gradiometers, signal space projection or homogeneous field correction. C_LI

Source connections

Explore related subjects

neurosciencePreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Bezsudnova, Y., Jensen, O.. 2023-09-22. Optimizing magnetometers arrays and pre-processing pipelines for multivariate pattern analysis. https://doi.org/10.1101/2023.09.21.558786

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

Single-cell RNA sequencing (scRNA-seq) captures detailed gene expression profiles at scale, while patch-clamp recordings measure intrinsic neuronal electrophysiological properties. Modeling the relations between these two modalities remains a challenge. Here, we compare how well electrophysiological features can be predicted by traditional transcriptomic cell type classification, representations derived from a foundational model (scGPT) pretrained on large-scale scRNA-seq datasets, ion channel-coding genes, and highly variable genes. Using paired transcriptomic and electrophysiological patch-sequencing data from 495 human neurons from neurosurgical tissue, we find that cluster-level cell type representations consistently outperform highly variable gene selection, ion channel gene selection, and context-enriched scGPT embeddings. Notably, performance varies across model architectures and initializations, and the best results are obtained by combining the outputs of separate cell type and scGPT-based models. Together, these findings suggest that traditional discrete cellular classification is highly effective in predicting physiological features. For maximum performance it can be complemented by pretrained transformer models.

neuroscience↗
bioRxiv2026

A nonlinear inhibition pathway underlying cortical responses to tuned holographic optogenetic perturbations

Optogenetics enables causal manipulation of cortical activity. Perturbation responses can be counterintuitive due to network interactions, making theory essential for predicting them. Existing approaches often rely on linear approximations, which fail for many biologically relevant perturbations. Here we develop a nonlinear theory of responses to holographic perturbations in cell-type-specific recurrent networks with structured connectivity. We fit a nonlinear model to mouse V1 data, which shows cotuned-ensemble suppression: perturbing spatially clustered neurons with similar preferred orientations yields markedly stronger short-range suppression than perturbing untuned ensembles. We show that cotuned-ensemble suppression arises from a feature-tuned, nonlinear inhibition pathway implicating somatostatin-positive (SST) interneurons. The theory predicts that cotuned ensembles suppress parvalbumin-positive (PV) neurons but facilitate SST neurons, and links the degree of cotuned-ensemble suppression or facilitation to the variance of the SST response. This framework identifies mechanisms by which nonlinear inhibition sculpts cortical dynamics and establishes a predictive basis for targeted optogenetic interventions.

neuroscience↗
bioRxiv2026

Proteomic signatures of APOE ε4 across human tissues and cell types in Alzheimers disease

The apolipoprotein E {varepsilon}4 (APOE {varepsilon}4) allele is the strongest genetic risk factor for late-onset Alzheimers disease (AD). However, the underlying molecular mechanisms remain unclear. This study included 1691 participants from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP), 1226 participants from the Accelerating Medicines Partnership - Alzheimers Disease (AMP-AD) Diverse Cohorts Study, and 735 participants from the Alzheimers Disease Neuroimaging Initiative (ADNI). To characterise APOE {varepsilon}4 molecular effects, we analysed proteomic data from plasma, cerebrospinal fluid (CSF), and induced pluripotent stem cell (iPSC)-derived astrocytes and neurons, as well as transcriptomic and proteomic data from multiple brain regions. The association of APOE {varepsilon}4 with AD neuropathology was also examined. APOE {varepsilon}4 carriers shared a plasma proteomic signature enriched for immune processes, irrespective of AD diagnosis. A machine learning classifier trained on this signature discriminated APOE {varepsilon}4 carriers from non-carriers in an independent cohort using CSF proteomics. APOE {varepsilon}4 carriage was associated with higher Braak stages and Consortium to Establish a Registry for Alzheimers Disease (CERAD) score. However, only limited APOE {varepsilon}4-associated transcriptomic and proteomic changes were observed in bulk brain tissue, with poor cross-layer concordance. Proteomic analyses of iPSC-derived astrocytes and neurons further revealed cell-type-specific APOE {varepsilon}4-associated changes. APOE {varepsilon}4 is associated with a consistent proteomic signature across plasma and CSF. Its molecular effects in the brain differ across cell types, brain regions and molecular layers. These findings support the need for cell-type-resolved multi-omic studies to elucidate how APOE {varepsilon}4 confers AD risk.

neuroscience↗