Just finished setting up a pipeline to run spaceranger segment for Visium HD nuclei segmentation QC on a Windows laptop using WSL2.

spaceranger segment must be run locally — 10x Cloud doesn't support it or maybe we can make a wish in the future — which is a barrier for labs without a dedicated Linux workstation, like me.

Took a while to figure out some gotchas (NTFS symlink errors on /mnt/, ~ not expanding in --tissue-image), so I documented the full workflow including a QuPath Groovy script for cropping the H&E region to the 6.5 × 6.5 mm Visium HD capture area.

Tested on 32 GB RAM (HP EliteBook 835, WSL2 Ubuntu 22.04) — works fine for segment even though the official requirement for the full pipeline is 64 GB.

GitHub: https://github.com/jychen74/visiumhd_qc_windows