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...

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

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...

Integrating gene expression and imaging data across Visium capture areas with visiumStitched www.biorxiv.org/content/10.1... 🧬🖥️ github.com/LieberInstit... #rstats

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! ^_^

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

Integrating gene expression and imaging data across Visium capture areas with visiumStitched https://www.biorxiv.org/content/10.1101/2024.08.08.607222v1

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

Integrating gene expression and imaging data across Visium capture areas with visiumStitched https://www.biorxiv.org/content/10.1101/2024.08.08.607222v1