Software

This repository provides a compact MATLAB/SPM12 implementation of representational-similarity analyses for navigation fMRI data. It includes a fully reproducible mock-data workflow that generates synthetic two-run BOLD data, event files, motion regressors, and example pmEC, retrosplenial cortex, and presubiculum ROIs. [...]

QCima Studio is a standalone software application for quality control of MACSima spatial proteomics datasets. It provides convenient access to review individual antibody signals alongside their corresponding background and autofluorescence reference images.Users can adjust visualization settings, classify signals as accepted or discarded, and automatically organize imaging data by scene (Rack–Well–ROI), antibody, and autofluorescence reference.The software is designed for fast, script-free QC workflows and supports session saving, analysis resumption, structured metadata review, and seamless transfer of QC decisions back to MACS iQ View..

QCima Studio is a standalone software application for quality control of MACSima spatial proteomics datasets. It provides convenient access to review individual antibody signals alongside their corresponding background and autofluorescence reference images.Users can adjust visualization settings, classify signals as accepted or discarded, and automatically organize imaging data by scene (Rack–Well–ROI), antibody, and autofluorescence reference.The software is designed for fast, script-free QC workflows and supports session saving, analysis resumption, structured metadata review, and seamless transfer of QC decisions back to MACS iQ View..

This repository contains the MATLAB/SPM12 analysis scripts that implement the first-level fMRI model and region-of-interest representational similarity analyses used to quantify six-fold grid-cell-like representations and their temporal stability across runs.The repository includes:A first-level GLM in which translation events are grouped into six directional phase regressors. Each regressor combines movement directions separated by 60°, producing phase offsets of 0°, 10°, 20°, 30°, 40°, and 50°.An ROI-based representational similarity analysis that extracts voxelwise beta patterns for the six phase conditions from each run.Calculation of run-specific neural representational dissimilarity matrices (RDMs) using correlation distance Calculation of a cross-run neural RDM and its Spearman correlation with a theoretical six-fold model RDM (grid-cell-like signal magnitude)Assessment of temporal stability as the Spearman correlation between the unique off-diagonal elements of the run-1 and run-2 neural RDMs (temporal stability metric)A fully synthetic mock dataset generator for testing the complete analysis pipeline.The mock dataset follows the main acquisition and task structure, with a repetition time of 2.2 seconds, two runs of 246 volumes, six motion regressors per run, semicolon-delimited event files, and a synthetic ROI mask. [...]

MotilA is a Python-based image analysis pipeline designed to quantify microglial fine process motility from 4D and 5D time-lapse image stacks acquired through multi-photon in vivo imaging. While developed for microglial analysis, MotilA can be applied to other cell types and imaging studies as well. [...]

This repository contains the code written by Pia Grundschöttel to analyze neurons from the hippocampus and cortex stimulated with IgLON5, IgG and PBS to reproduce the results of the manuscript Askin et al., Science Advances, 2026.Additional information can be requested by the authors and data is available under the following GEO accession numbers: GSE298951..

This is an accompanying repository to the R package metadeconfoundR. It contains the procedure for benchmarking Maaslin2/3 and metadeconfoundR using sparseDOSSA2 generated simulations of gut microbial abundance data as part of the metadeconfoundR publication..

Code repository for "Axon initial segment dynamics during associative fear learning"..