Xenium catalyst experiment, on mouse brain (248 gene panel) and lung (379 atlasing panel)




Xenium catalyst experiment-onboard analysis
Xenium catalyst experiment-onboard analysis




xenium_workflow




Xenium Segmentation using combined nuclei, boundary and content staining


Layout of tissue sections




Sample images




Sample layouts




Culstering of brain section cells


Clustering of mutliple tissues


Xenium workflow


Tissue section layout


Summary of Xenium spatial data


Transcripts density in a brain section


Transcripts density in a lung and cerebellum section


Clusters of sham-TBI section


Clusters of sham-TBI section on umap embeddings


nuclei and cell stain for segmentation


nuclei stain for segmentation


Supervised annotation for cell types-brain cortex


Transcripts-1


Transcripts-2


Transcripts-3


Summary of one lung section data


Unsupervised clustering of the lung





Segmentation of lung cells


Unsupervised clusters of the mouse lung


Supervised clustering of the mouse lung


Lung cells overlaid on HE staining


Brain and nodose gangalia


Another summary of experiment


Lung section with transcripts-1


Lung section with transcripts-2


Slide 1 layout



Slide 2 layout