Code Archive

Pipeline and code are available for imaging data preprocessing using a micro-fiber array approach to measure and manipulate local dynamics in mice, allowing the study of cell-specific signals in 3D volumes.

Pipeline and MATLAB code for a micro-CT-based method for precise fiber localization and atlas alignment after performing micro-fiber photometry in behaving mice.

All original G-code used to jet-print the microfluid-walled dumbbells described in Nebuloni, F. et al. (2024) study.

Code for snRNAseq dataset analysis of AAV-infected mouse olfactory epithelium. This code accompanies the manuscript: Comparative Analysis of AAV Serotypes for the Transduction of Olfactory Sensory Neurons by Belfort, Jia et al. 2024.

Scripts by Jeffrey Stedehouder and Professor Kevin McGerty to analyze and plot FCV and patch-clamp experiments in ex vivo mouse brain slices and to model the distance between cell types.

The project investigates if immune cells impact neurodegenerative diseases differently based on ancestry. It examines disease gene expression and genetic links in African, East Asian, and European populations.

An analytical tool to be used with the 10X Visium Platform to compare spatial gene expression values.

R scripts for the statistical analysis and plotting in the paper GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes.

This script calculates a directionality index to assess the randomness of cell movement.

This script assesses the complexity of extracellular matrix network through a skeleton analysis.

This repository contains MATLAB scripts and utilities for the analysis of simulated and experimental POLCAM single-molecule orientation-localisation microscopy (SMOLM) data using RoSE-O, providing accurate and precise measurements of the location and orientation of single molecules.

A napari plugin to process and render polarization camera data.

MATLAB Code: for live polarization camera image processing.

Software for processing single-molecule and diffraction limited polarization camera image data.

MATLAB Code: cameraCalibrationCMOS: v1.1.

All original R code written to analyze results shown in SpatialBrain.org and Kilfeather & Koo et al. (2024), "Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease."

Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.

CREsted offers detailed analyses and tutorials for studying enhancer codes and creating synthetic enhancer sequences at cell type-specific, nucleotide-level resolution.

Code for PD progression survival GWAS to mortality, and Hoehn and Yahr stage 3 or greater (H&Y3+) to understand the determinants of mortality and motor progression in Parkinson’s disease.

Code used for the analysis of clinical data as reported in the study, "Persistent Hyposmia as Surrogate for α-Synuclein-Linked Brain Pathology" in Mollenhauer, Li et al., MedRxiv 2023.