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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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Determining spatial.factors for CurioSeeker platform in creating a CellChat object #84

Open strawberry098 opened 9 months ago

strawberry098 commented 9 months ago

Given CurioSeeker Slide-seq version 2 is based on 10 um beads (almost single-cell resolution), how can I determine spatial.factors?

sqjin commented 9 months ago

@strawberry098 Please check the "FAQ for other spatial technologies"

ShaowenJ commented 9 months ago

Hi @sqjin , why the conversion.factor = 0.73? based on the Slide-seq paper and its method, isn't the conversion factor is 1.54?

sqjin commented 9 months ago

@ShaowenJ @strawberry098 So this is sample-dependent? Below is the one where I get the conversion factor information

image
ShaowenJ commented 9 months ago

Hi @sqjin ,for From the original Slide-seq v2 paper github https://github.com/rstickels/Slide_seqv2/blob/master/SlideseqV2_visium_comparison_submission.ipynb In the 18th chunk, they have a conversion factor between the pixel and micrometer, which I guess would be the conversion factor 1.54 Just curious, What software for the image you were showing?

ShaowenJ commented 9 months ago

Also, I am very unsure about how should we set up the scale.distance for the slide-seq data? in the computeCommunProb function? Sorry for bringing this up in this question.

ShaowenJ commented 6 months ago

Any updates from this question? @sqjin Thanks!