Top row shows spots from a blue (fill) and a green (border) capture area before using visiumStitched. Once you've stitched the data together, BayesSpace and PRECAST will find up to 12 neighbors for a spot of interest by using the array/row hex grid information: 6 blue ones and 6 green ones.

Here's an improved diagram for how #visiumStitched is able to help #BayesSpace, #PRECAST, and other array-based methods (col/row from the hex grid) find more neighboring spots when you have overlapping spots from different capture areas.

You already generated the 🤩 data, might as well use it! ^_^

Spatial cluster matching rate among overlapping spots improves when using visiumStitched. It's also better for highly variable genes (HVGs) used as input to BayesSpace, and with spatially variable genes (SVGs) identified with nnSVG when using PRECAST.

One 💯 update is how @nick-eagles.bsky.social used the overlapping spots to calculate a matching rate in spatial cluster assignments

#BayesSpace with HVGs does better, whereas #PRECAST with #nnSVG SVGs does slightly better. Both improve when using #visiumStitched to increase the number of neighbors

I'm thrilled to share with you that #visiumStitched led by @nick-eagles.bsky.social has now been published

Our #RStats / @bioconductor.bsky.social 📦 provides a framework for stitching together multiple #Visium @10xgenomics.bsky.social capture areas together

#AcademicSky

doi.org/10.1186/s128...

Today at @libdrstats.bsky.social we did some live debugging on 2 #Bioconductor 📦s we submitted

* #visiumStitched: we tried reproducing a Single Package Builder error
* #DeconvoBuddies: we discussed options to comply with the 15 min limit to "R CMD build"

#RStats

youtu.be/YAeUsKGUmtM

It can handle > 2 capture areas, adjacent ones, & facilitates downstream spatially-aware clustering with methods that use the array col / row hex grid information such as #BayesSpace & #PRECAST

The proportion of matches on overlapping spots increases 📈with #visiumStitched

Is your tissue larger than a #10xGenomics Visium capture area? If you need to stitch together the images but also the gene expression data, check our new preprint describing #visiumStitched

We also shared example postmortem human brain data (3 samples)

doi.org/10.1101/2024...