Outlier waveform detection for internal globus pallidus (GPi) activity
By onMatlab code identifies single units with spike waveforms that take on outlier feature values in the internal segment of the globus pallidus (GPi) units recorded from two nonhuman primates (in healthy and parkinsonian states).
Code for: Dissociation of putative open loop circuit from ventral putamen to motor cortical areas in humans I: high-resolution connectomics
By onCode for pre-processing fMRI data and region on interest masks associated with Rixor et al. 2024.
BIDCell to Seurat
By onThis repository contains an enabler script to convert the BIDcell segmentation output to a Seurat object for the processing of 10X Genomics Xenium spatial transcriptomics data.
TULIP – mulTiome demultiplexing Using Long-read SNP Information Pipeline
By onSnakemake pipeline to demultiplex 10x multiome data utilizing SNP calls from WGS sequencing of pooled patients.
Multiome preprocessing seurat
By onWorkflow to preprocess single nucleus multiome data (gene expression + ATAC) produced with 10X Genomics Cellranger ARC in Seurat.
Computational analysis for “Comparative Analysis of AAV Serotypes for the Transduction of Olfactory Sensory Neurons” by Belfort and Jia et al. 2024
By onCode 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.
Custom Python and MATLAB scripts related to Stedehouder & Roberts (2024) “Rapid modulation of striatal cholinergic interneurons and dopamine release by satellite astrocytes”
By onScripts by Jeffrey Stedehouder, Stefania Vietti-Michelina & Professor Kevin McGerty to analyse and plot FCV, patch-clamp, and GRAB sensor imaging experiments in ex vivo mouse brain slices, and to model the distance between cell types.
Python script for analyzing Prairie View 5-generated .csv files of BOT imaging data
By onPython script for analyzing Prairie View 5-generated .csv files of BOT imaging data in Figures 5 and S2 of Zhai et al 2025.
Python script for analyzing Prairie View 5-generated .csv files of dendritic excitability data
By onPython script for analyzing Prairie View 5-generated .csv files of dendritic excitability data in Figures 1, 3, 6, 7 in Zhai et al 2025.
Python script for analyzing Prairie View 5-generated .csv files of somatic excitability data
By onScript used to analyze somatic excitability data in Figures 1, 3, 6, 7 and 8 of Zhai et al 2025.
SNr subpopulation neuroanatomy-code
By onMatlab scripts used to plot anatomical data related to the study: Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses.
Baseline α–synuclein Seeding Activity and Disease Progression Code
By onThe project analyzes baseline α-synuclein seeding activity and Parkinson's disease progression.
Custom MATLAB scripts related to Zhang, Y. et al (2025) “An axonal brake on striatal dopamine output by cholinergic interneurons”
By onMATLAB scripts written by Yan-Feng Zhang to predict how nicotinic receptors impact on dopamine transient in vivo during the dynamic tonic and multiphasic activity in cholinergic interneurons.
Calcium and Behavior Video Alignment Scripts for Open-Field Dyskinesia Analysis (Alcacer et al., Cell Reports 2025)
By onMatlab scripts for alignment of calcium imaging videos and videos from mice in an open field arena recorded from a bottom camera from Alcacer et al. 2025.
TRAP In Vivo Analysis
By onGitHub Code and data from Ryan et al., 2024. Includes TRAP_InVivo_Analysis.m for Plexon MAP data analysis, TRAP_Remove_INs.m for removing putative interneurons, and Summary.mat containing behavior/electrophysiology data used for Figures 1 and S1.
TRAP-Rabies-Analysis
By onStudy by Ryan et al., 2024 used mice injected with viruses to label neurons in the brain. Resource is GitHub code with Rabies_Analysis.m to analyze data to map neurons and Rabies_Summary.mat contains normalized data for figures 2 and S2.
Open Field Analysis
By onA Python script processes open field analysis data from an excel sheet to calculate average velocity,rotations, and distance moved. The output is stored in a 'Metrics' spreadsheet, cross-checked with manually computed metrics in another sheet.
Code-Sheng et al 2025
By onCustom Matlab and Labview code used in analysis in Sheng et al 2025 paper.
nix-lir-binding-to-wipi2d
By onScripts used to analyze molecular dynamics simulations of NIX bound to WIPI2d in the following publication: https://doi.org/10.1101/2024.08.28.609967
Matlab code: Determination of precisely timed sequences of calcium events
By onThe file "Identify_sequences.m' used to identify sequences of calcium imaging events.
