Read in VisiumHD cell segmentations from SpaceRanger 4.0+

[MicTott]

Hi all,

You may already know this, but SpaceRanger 4.0 released a few weeks ago which includes new functionality to perform cell segmentation on the H&E images. This uses a custom trained StarDist model to segment H&E images.

The readVisiumHD is currently not compatible with the new segmented outputs, so I just wanted to share this here and bring it to the team's attention. I imagine this will be a popular pipeline for acquiring cell segmentations in VisiumHD.

Thanks for the all of the awesome work on SFE!

Best,
Michael

[estellad]

Hi @MicTott ,

I just came up with a solution.

Please see the utils I made here: https://github.com/estellad/EuroBioC2025OSTAWorkshop/blob/devel/vignettes/utils.R
Complete use case: https://estellad.github.io/EuroBioC2025OSTAWorkshop/articles/seq-workflow-visium-hd-cell.html

Sincerely,
Estella

[MicTott]

Hi Estella,

Thanks so much for developing this! It's going to be a huge help.

All the best,
Michael

[estellad]

You are welcome! Glad I figured it out before the EuroBioC OSTA workshop too 😊

Estella