RoSE-O_POLCAM
By onRoSE-O adapted for SMOLM using polarization camera. Can also be modified to work with other single-channel imaging systems.
Preprocessing pipeline to establish and extract data from ROIs from multifiber photometry movies
By onPipeline and code are available for imaging data preprocessing using a micro-fiber array approach to measure and manipulate local dynamics in mice, allowing study of cell-specific signals in 3-D volumes.
Custom G-code used to jet-print microfluid-walled dumbbells
By onAll original G-code used to jet-print the microfluid-walled dumbbells described in Nebuloni, F. et al. (2024) study.
R scripts associated with SpatialBrain.org
By onAll original R code written to analyse 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".
Pipeline and MATLAB scripts for micro-CT-based fiber localization
By onPipeline and MATLAB script for micro-CT-based method for precise fiber localization and atlas alignment after performing micro-fiber photometry in behaving mice.
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.
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).
Multiome preprocessing seurat
By onWorkflow to preprocess single nucleus multiome data (gene expression + ATAC) produced with 10X Genomics Cellranger ARC in Seurat.
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.
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.
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.
HYX990205/ReRx: Drug Repurposing for Parkinson’s Disease
By onToolkit for drug repurposing analysis used in the preprint: "Drug Repurposing for Parkinson's Disease: A Large-Scale Multi-Cohort Study" Find more at https://doi.org/10.1101/2025.05.20.25327943.
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.
