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.
Matlab code: Event-based analysis of calcium transients
By onMatlab algorithms to align raw calcium traces to behavioral events during a behavioral task.
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.
