Hi everyone,
I’m working with spatial transcriptomics data in Seurat but only have these files:
filtered_feature_bc_matrix.h5
tissue_hires_image.png
tissue_positions_list.csv
scalefactors_json.json
I need to generate tissue_lowres_image.png because my system can’t handle the high-res image because I'm working with multiple tissues, is there a tutorial on how to downscale tissue_hires_image.png or how to create the tissue_hires_image.png?
Either Python or R will be fine
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Genomancer •
Is this 10x spatial data? File names seem to indicate so. While someone provides an answer this is what 10x support says about the tissue images.
https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs
my system can’t handle the high-res image because I'm working with multiple tissues
As in you don't have enough memory?
It looks like Seurat can handle high-res images based on this comment --> https://github.com/satijalab/seurat/issues/5614#issuecomment-2105263800 but that is likely not the question you are asking.
sorry for the incomplete question. Yes, its 10x spatial data and I'm having trouble comparing the multiple tissues because I don't have enough memory I used the calculations in the 10x support in the link you provided and I was able to solve the problem. thanks
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