Software

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"..

Spintge, Mai, Carraro et al., 2026: Single-cell multi-omic profiling allows the dissection of peripheral immune phenotypes in Alzheimer’s Disease progression The role of the peripheral immune system in Alzheimer’s Disease (AD) remains insufficiently resolved, limiting the understanding of systemic disease effects and mechanisms. Here, we employed three high-resolution single-cell techniques, including flow cytometry, single-cell RNA- and ATAC-sequencing, to investigate peripheral immunity in AD dementia and earlier stages of the AD trajectory in over 100 patients. [...]

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. The tools in this software implement various reconstruction algorithms for Magnetic Resonance Imaging. [...]

PyMyelinPSO version 1.0 is a Python framework for Particle Swarm Optimization (PSO)–based inversion of in-vivo and atlas MRI data (published by Dvorak et al., (2021). An atlas for human brain myelin content throughout the adult life span. [...]

Toolbox of Snakemake pipelines for easy-to-use analyses and benchmarks for building integrated atlases. This toolbox provides multiple modules that can be easily combined into custom workflows that leverage the file management of Snakemake. [...]

This is the analysis code used in our project on mean longitudinal resting-state and task functional connectivity within and between medial temporal lobe and posteromedial cortex in the PREVENT-AD cohort..