Software & Data

Open data resources and software tools from my work. Everything here is public — the interactive browsers need nothing but a web browser.

Data resources

Human amygdala spatial transcriptomic atlas

Spatially-resolved transcriptomics of the postmortem human amygdala across three 10x Genomics platforms — Visium (n = 7 donors), Xenium (n = 4), and Visium HD (n = 5 capture areas). The interactive browsers are powered by Vitessce.

All browsers · Visium · Xenium · Visium HD · One donor, all three platforms

Code · Raw data: GSE342709 (Visium), GSE342289 (Xenium), GSE342738 (Visium HD)

Cross-species basolateral amygdala snRNA-seq

Single-nucleus RNA sequencing of amygdala subregions (LA, BA, aBA, CeA) in human (n = 5), rhesus macaque (n = 5), and olive baboon (n = 2). Split into one iSEE app per species so each stays responsive.

Human · Macaque · Baboon

Code · Processed data (Globus) · Raw data: GSE281366 · Paper

Software

SpotSweeper

Spatially-aware quality control for spatial transcriptomics. Detects local outlier spots and regional artifacts by comparing each spot to its spatial neighbors, rather than to the sample as a whole.

Bioconductor · Code · Paper

SpotSweeper-py

The SpotSweeper quality control metrics for the Python/scverse ecosystem.

PyPI · Code · Paper

FrozenPy

A Python package for quantifying freezing behavior in rodents from raw locomotor traces.

Code

FiberFlow

A Streamlit app for analyzing fiber photometry data.

Code