There is Minecraft. And then there is the #Visium manual fiducial alignment

#SpatialTranscriptomics #BioInformatics

Excited for participating in this #spatialtranscriptomics #Visium platform study with an expert team from @NICHD_NIH, in the first step of studying the spatial biology of #pituitary corticotroph tumors, revealing their heterogeneity.

https://www.medrxiv.org/content/10.1101/2023.08.04.23293576v1

Alignment of spatial transcriptomics data from different platforms by Jean Fan group
https://www.biorxiv.org/content/10.1101/2023.04.11.534630v1
#spatialtranscriptomics #xenium #visium #bioinformatics

Use visium to predict missing genes in xenium #spatialtranscriptomics #geneimputation #bioinformatics #xenium #visium
https://www.biorxiv.org/content/10.1101/2023.02.07.527488v1

Our work to derive hidden knowledge from #spatialtranscriptome by deep learning (DeepSpaCE) was one of the top 100 downloaded cancer papers for Scientific Reports in 2022!

According to https://www.nature.com/collections/ciijehjfha, our paper was ranked 9th in the cancer papers. I will continue to work on developing new methods to encourage data-driven science!

Paper: https://nature.com/articles/s41598-022-07685-4
Tool (DeepSpaCE): https://github.com/tmonjo/DeepSpaCE (ready-to-use for #Visium data).

RT @lahuuki
Hot of the pre-print press! 🔥 Our latest work #spatialDLPFC pairs #snRNAseq and #Visium spatial transcriptomic data in the human #DLPFC building a neuroanatomical atlas of this critical brain region 🧠
@LieberInstitute @10xGenomics #scitwitter
📰 https://doi.org/10.1101/2023.02.15.528722

COMMOT, COMMunication analysis by Optimal Transport, a versatile tool infer cell–cell communication in #SpatialTranscriptomics 🤠

Compatible with #MERFISH #Visium seqFISH+ #STARmap

vs #CellChat #Giotto #CellPhoneDBv3

Dr. Qing Nie lab Nature Methods 2023
https://www.nature.com/articles/s41592-022-01728-4

RT @Ellorebo@twitter.com

Thrilled that our Spatial ATAC manuscript is now out @NatureBiotech@twitter.com 
Open: https://www.nature.com/articles/s41587-022-01603-9

We repurposed the #Visium platform @10XGenomics@twitter.com to capture and profile open chromatin with spatial resolution in tissue sections from mouse and human. https://twitter.com/MargheritaZamb2/status/1553705646154989569

🐦🔗: https://twitter.com/Ellorebo/status/1611044290985066497

RT @Ellorebo
Thrilled that our Spatial ATAC manuscript is now out @NatureBiotech 
Open: https://www.nature.com/articles/s41587-022-01603-9

We repurposed the #Visium platform @10xGenomics to capture and profile open chromatin with spatial resolution in tissue sections from mouse and human. https://twitter.com/MargheritaZamb2/status/1553705646154989569

RT @Ellorebo
Thrilled that our Spatial ATAC manuscript is now out @NatureBiotech 
Open: https://www.nature.com/articles/s41587-022-01603-9

We repurposed the #Visium platform @10xGenomics to capture and profile open chromatin with spatial resolution in tissue sections from mouse and human. https://twitter.com/MargheritaZamb2/status/1553705646154989569

RT @Ellorebo@twitter.com

Thrilled that our Spatial ATAC manuscript is now out @NatureBiotech@twitter.com 
Open: https://www.nature.com/articles/s41587-022-01603-9

We repurposed the #Visium platform @10XGenomics@twitter.com to capture and profile open chromatin with spatial resolution in tissue sections from mouse and human. https://twitter.com/MargheritaZamb2/status/1553705646154989569

🐦🔗: https://twitter.com/Ellorebo/status/1611044290985066497

RT @Ellorebo@twitter.com

Thrilled that our Spatial ATAC manuscript is now out @NatureBiotech@twitter.com 
Open: https://www.nature.com/articles/s41587-022-01603-9

We repurposed the #Visium platform @10XGenomics@twitter.com to capture and profile open chromatin with spatial resolution in tissue sections from mouse and human. https://twitter.com/MargheritaZamb2/status/1553705646154989569

🐦🔗: https://twitter.com/Ellorebo/status/1611044290985066497

Sneak peak on #visium analysis of advanced #pancreaticcancer

#spatialtranscriptomics #SpatialBiology