microglia

A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial cells.

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease of the adult, characterized by degeneration of motor neurons in the spinal cord, brain stem and motor cortex. There is no bio-informatic model of ALS.

Pipeline for analyzing microglial fine process motility from 4D/5D multi-photon imaging data

Sholl analysis pipeline for microglial branching, with patch-wise CLAHE preprocessing

Cross-species validation of AD microglial signatures using SEA-AD human brain single-cell data

ImageJ macro for morphological analysis

Graph-JEPA framework for SEA-AD Alzheimer microglia: pathology-grounded representation learning, donor-held-out validation, and counterfactual gene-network hypothesis generation.

Modular DESeq2 downstream pipeline — tximport, outlier detection, VST, PCA, volcano plots | Applied to APP/PS1 microglial bulk RNA-seq (BWH) | R

Thymus-derived myeloid education signatures (MES): single-cell + spatial transcriptomics pipeline mapping thymic immune programs to microglial tolerance positioning under glucocorticoid stress.

Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer’s disease.

Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital

snRNA+snATAC multiome of AD DLPFC microglia — chromVAR motif analysis, WNN integration, peak-to-gene linkage, Monocle3 trajectory | Signac · Seurat · R

Scripts to segment microglia images and generate reports

A curated and reproducible atlas of mathematical and computational models for neurons, astrocytes, microglia, oligodendrocytes, Schwann cells, and other nervous-system cell types.

A provenance-aware atlas of public human brain regulatory genomics: chromatin accessibility, histone marks, TF binding, methylation, 3D contacts and genetic regulation.

gHH: Generalised Hodgkin–Huxley Model

ImageJ macros to analyse microglial cells in live or fixed tissue (Work-in-progress)

In Alzheimer’s disease, abnormal levels of the Aβ protein aggregate together to form Aβ plaques. The response to plaques by microglial cells is characterised by changes in gene expression and an increase in cell density surrounding plaques. This set of semi-automated macros calculates both microglial density and changes in protein expression int…

Analysis code for Robust fluorescence-activated microglia enrichment from human post-mortem brain (Gocmanac, Dash, Nagaeva & Skene; UK Dementia Research Institute, Imperial College London).

Spatial Statistics and Explainable Deep Learning framework for Cell-Protein Interaction Profiling in Parkinson's disease