##Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix




Illustration of one Visium HD experiment. 8um bin size. Visium HD is released by TXG in April 2024.

Visium HD data illustration



Illustration of one Xenium imaging spatial experiment. Using a pre-built mouse brain panel of 248 probes. Two hemisections are included (control, mutant/treated). In addition, two brain stem and six nodose ganglia sections were included.

Xenium imaging based data illustration, on UMAP and spatial embeddings


Visium HD spatial transcriptomics, with unsupervised clustering, 2000K cells!!

One visium slide, A1 imaging area, 200K cells


Maginified view of one PFC section of A1 imaging area.

One Visium slide, A1 imaging area, one section zoom, with unsupervised clustering
One Visium slide, A1 imaging area, one section zoom, with unsupervised clustering




Look at the detected spots that are spot on cell soma!! Amazing resolution…

Unsupervised clustering of PFC cells


This is the brain cell HE staining for the above image.

HE-stained tissue image for the above image


Note cell soma ALWAYS has highest UMI counts!

UMI numbers overlaid on the tissue image


This is the sample image for the above, note soma location exactly overlap with highest UMI spots!

Unsupervised clustering of PFC cells
Unsupervised clustering of PFC cells




Xenium imaging of a nodose ganglia (what do you think it look like??)

Xenium imaging of a nodose ganglia


Xenium imaging of a nodose ganglia - cell segmentation

Xenium imaging of a nodose ganglia- cell clustering
Xenium imaging of a nodose ganglia- cell clustering




Xenium imaging of a nodose ganglia - transcripts overlaid on soma

Xenium imaging of a nodose ganglia- in situ transcripts signal
Xenium imaging of a nodose ganglia- in situ transcripts signal