Research software
We develop open and reproducible software tools that turn complex microscopy datasets into quantitative measurements of cells, tissues, and neural structures.
Deep-learning pipeline for restoration, segmentation, and quantitative analysis of dendritic spines, branches, and soma. RESPAN uses content-aware restoration to improve signal, contrast, and isotropic resolution in volumetric microscopy datasets, including live imaging and in vivo two-photon datasets.
3D image analysis pipeline for quantifying cells, nerves, and local tissue environments in neural and skin tissues. QLEAN supports per-cell measurements, image-level summaries, spatial analysis, and statistical comparisons across hindpaw skin, dorsal root ganglion, spinal cord, and in vitro culture datasets.
Fiji-based workflow for stitching, alignment, and analysis of serial whole-brain section imaging. BrainJ supports atlas registration, region-level quantification, and mesoscale mapping of axons, dendrites, and labeled cell populations.
Fiji-based workflow for serial-section alignment, atlas-guided region segmentation, and 3D analysis of cells and neuronal projections in whole spinal cord datasets. SpinalJ was developed as an extension pipeline to BrainJ for spinal cord mapping.