Software
Open-source tools I’ve built or contributed to for spatial and imaging-based transcriptomics. More on my GitHub.
Off-target Probe Tracker (OPT)
A tool associated with the Xenium off-target probe binding work for identifying putative off-target probe binding through sequence-alignment-based analysis.
P-Het
Software for Preserving Heterogeneity / subtype discovery from transcriptomic data, associated with the Nature Communications P-Het paper.
SpatialMNN
spatialMNN, an algorithm that integrates multiple spatial transcriptomic samples and identifies spatial domains.
STARIT
Converts transcripts within segmented cells in imaging-based spatial transcriptomics data into rasterized image tensors, enabling deep-learning models to characterize cell states from subcellular molecular heterogeneity rather than gene counts alone.
FNA-Net
Deep learning software associated with FNA-Net for screening the adequacy of unstained thyroid fine needle aspiration samples.