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SpatialTranscriptomicsResearch / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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overlay molecular data on top of tissue histology #117

Closed WT215 closed 4 years ago

WT215 commented 4 years ago

Hello,

Now I have a PNG of tissue histology and coordinates of spots. How could I overlay the molecular data on top of tissue histology like shown in Seurat's tutorial https://satijalab.org/seurat/v3.1/spatial_vignette.html?

Data come from https://spatialtranscriptomics.com/resources/

Thanks a lot!

haowBio commented 1 year ago

I meet the same issue, how you deal with it?

WT215 commented 1 year ago

I meet the same issue, how you deal with it?

Use spaceranger to preprocess the fastq files (if you are using 10X visium).