Microglial transcriptomes in acute neurodegeneration
Bulk and single-cell RNA-sequencing data from Tay et al. 2017 and Tay et al. 2018.
AutoMorFi: Automated Whole-image Morphometry in Fiji/ImageJ for Diverse Analyses and Discoveries
Works for glia, neurons, other cell types, organisms, and even objects such as corallites! Click here for the preprint
Automated single-cell and tissue analysis using CellProfiler pipelines unveil context-dependent heterogeneity of the central nervous system
Coming soon! Check back again. (Planned release: September 2025. Contact us for code and collaborations.)
Whole-image spatial integration of single-cell marker and morphology by CellCompiler
Coming soon! Check back again. (Planned release: November 2025. Contact us for code and collaborations.)
U-Net – Deep Learning for Cell Counting, Detection, and Morphometry
For (semi) automated detection and counting of biological objects in large datasets. Works for glia too! Publication
ImageJ / Fiji HDF5 Plugin
For loading, writing and storing of extremely large and complex image datasets.
XuVTools
A fully automated 3D stitching software for biomedical image data (confocal microscopy images). Publication