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.
Code used in “Lrrk2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis”
By onUsing scRNAseq and flow cytometry, we demonstrated that the Lrrk2-G2019S mutation is associated with an increased neutrophil presence in the colonic lamina propria, Th17 skewing, upregulated Il17a, and greater colonic pathology during infection.
Custom scripts related to Graziano, M. et al. (2025) “A molecular atlas of cell-type specific signatures in the parkinsonian striatum”
By onScripts by Graziano and Masarapu aid in analyzing single-nucleus RNA sequencing data from Parkinson's Disease striatum, mapping vulnerabilities, and inferring cell trajectories. Giacomello Lab scripts are available on GitHub.
Collection of command-line Python-based scripts for voxel-wise computation
By onCollection of command-line Python-based scripts for voxel-wise computation
Script for rat brain images processing
By onScript for rat brain images processing used in https://doi.org/10.1101/2024.10.22.619619
Version 1.0 Neuromelanin quantification R scripts
By onVersion 1.0 release of Neuromelanin quantification R scripts
Generation of knock-in Cre and FlpO mouse lines for basal ganglia and dopamine neuron investigation (CODE)
By onThe software contained in this repository was used to analyze the whole-cell electrophysiology recordings of striatal spiny projection neurons and midbrain dopamine neurons.
Code R script related to doi.org/10.1038/s41531-025-01063-3
By onSevere GBA1 variants are linked to Parkinson's disease, impacting counseling and clinical trials. Access R script at doi.org/10.1038/s41531-025-01063-3 for more details.
Bolen CosMx human Colon RNA and Protein code
By onRepository for the paper "Spatial single-cell multiomics..." includes CosMx assays, README files with scripts/data for analysis, and computational environment requirements. It also features a tissue microarray image showing morphology markers.
BrainLysoAtlas
By onSummary: Research by Ghoochani et al. presents a code repository linked to their study on brain lysosomes, identifying SLC45A1-related disease as a lysosomal disorder.
