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BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data
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diameter size in xenium tutorial #250

Closed revolvefire closed 10 months ago

revolvefire commented 1 year ago

Thanks for the wonderful tool!

I've been working on the xenium data and I wasn't 100% sure what exactly "spot_diameter_fullres" means in the xenium tutorial

Does the number for this parameter means the diameter of the spot(circle) from which all the transcripts are taken into account as those for a cell?

So from an x,y coordinate that xenium provides for each cell (that it thinks is a cell, based on the DAPI image) stlearn will take into account all the transcript within the circle with a diameter of 15um (perhaps the center would be the exact x,y coordinate)? am I getting at it correctly?

Thanks!

duypham2108 commented 1 year ago

It does not mean that actually. The Xenium (computational) protocol did the transcript count already. The "spot_diameter_fullres" parameter serve for other automatic calculation like neighborhood finding in CCI analysis. You don't need to worry about it

SGIlabes commented 12 months ago

Thank you for creating such a wonderful package. I am finding it very useful. And I have a similar question. The term 'spot_diameter_fullres' is described as 'The number of pixels that span the diameter of a spot in the original, full-resolution image.' (in 10X visium). So I'm wondering, is the reason for setting 'spot_diameter_fullres' to 15 for the convenience of computer calculations? Theoretically, should the 'spot_diameter_fullres' be 1 instead?

duypham2108 commented 12 months ago

Yes, we set 'spot_diameter_fullres' to 15 just for convenience, but it should not be used in Xenium data. The term 'spot_diameter_fullres' is created for spot-based data only. It could be useful only if you bin the Xenium data and the value should be your binning size

SGIlabes commented 12 months ago

Thanks!

Yes, we set 'spot_diameter_fullres' to 15 just for convenience, but it should not be used in Xenium data. The term 'spot_diameter_fullres' is created for spot-based data only. It could be useful only if you bin the Xenium data and the value should be your binning size