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.
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.
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.
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
suny-downstate-medical-center/pd_m1_6ohda: M1_Control_6OHDA
By onLiqiang Chu et al found decreased excitability in these neurons in a Parkinson's mouse model. A simulation using NetPyNE was created to study the impact of the changed PT5B neuron on motor cortex spiking dynamics.
Matlab code: Event-based analysis of calcium transients
By onMatlab algorithms to align raw calcium traces to behavioral events during a behavioral task.
Matlab code: Determination of precisely timed sequences of calcium events
By onThe file "Identify_sequences.m' used to identify sequences of calcium imaging events.
Script for image quantification [Wang et al 2025]
By onScript for image quantification used in Wang et al 2025
Python code: Figure generating script [Hanna et al 2024]
By onPython code: Figure generating script used in the preprint Hanna et al 2024
ImageJ code: Analysis script_0 [Hanna et al 2024]
By onImageJ code: Analysis script_0 used in the preprint Hanna et al 2024
SIFT based MATLAB script [Hanna et al 2024]
By onSIFT based MATLAB script used in the preprint Hanna et al 2024
Tailored workflows for the analysis of transposable elements (Garza et al, 2025)
By onGarza et al. (2025) created customized workflows for transposable element analysis across various data types. Workflows are in Snakemake, Jupyter notebooks, R markdowns, and scripts. Details are in the GitHub README.
Custom MATLAB scripts related to Bouabid, S. et al. (2025) “Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations”
By onMATLAB scripts written by Safa Bouabid to analyse ACh release dynamics, DA release, glutamate release onto cholinergic interneurons, and behavioural changes in mouse striatum during learning and extinction of Pavlovian associations.
Custom Phyton scripts related to Bouabid, S. et al (2025) “Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations””
By onPhyton scripts written by Safa Bouabid and adapted from Han Lab for reading 2D treadmill ball velocity with Raspberry Pi.
