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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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Spot diameter of 10X visium #92

Open oghzzang opened 6 months ago

oghzzang commented 6 months ago

Dear @sqjin

Hi, I'm a big fan of your program. However, I have just two questions.

Q1. Spot diameter

The spot diameter of 10X visium is 55um. This is the note from 10X genomics.

"Answer: The capture area is 6.5 x 6.5 mm. There are a total of 4992 total spots per capture area and each spot is 55 µm in diameter with a 100 µm center to center distance between spots." (Ref: https://kb.10xgenomics.com/hc/en-us/articles/360035487572-What-is-the-spatial-resolution-and-configuration-of-the-capture-area-of-the-Visium-v1-Gene-Expression-Slide)

But your program said it to "65" in the tutorial. Do you have any other meaning about that?

Q2. When I ran the following steps, the min value was so different with 100um.

It was 70um for spot.size =55. Then, should I edit the conversion.factor arbitrarily? If it's right, how can I change the conversion.factor and tol value?

scalefactors = jsonlite::fromJSON(txt = "scalefactors_json.json") spot.size = 55 # 65 in tutorial, the theoretical spot size (um) in 10X Visium conversion.factor = spot.size/scalefactors$spot_diameter_fullres spatial.factors = data.frame(ratio = conversion.factor, tol = spot.size/2) d.spatial <- computeCellDistance(coordinates = spatial.locs, ratio = spatial.factors$ratio, tol = spatial.factors$tol) min(d.spatial[d.spatial!=0]) #this value should approximately equal 100um for 10X Visium data

Thank you. Best,

Oh.

sqjin commented 6 months ago

@oghzzang You can check the information here

oghzzang commented 6 months ago

Yes, I'll check it! Thank you so much @sqjin.

Then, when I set 65um for visium spot.size, I couldn't get the min value (100um).

min(d.spatial[d.spatial!=0]) #this value should approximately equal 100um for 10X Visium data

It was 92.XX. My spot was derived from Visium CytAssist. Do you have any idea?

Thanks a lot. Best, Oh.

sqjin commented 6 months ago

@oghzzang It seems similar to Visium (https://ostr.ccr.cancer.gov/emerging-technologies/spatial-biology/visium/). I did not run cellchat on Visium CytAssist before. You may can find an example dataset form the 10X website and see if it holds. Yours is close to 100um, which should be ok. But it is better to figure out the reason.

oghzzang commented 6 months ago

Dear @sqjin,

I'm contacting with 10X genomics team about this issue. If you want to know the reason, I'll share it with you!

Thank you.

sqjin commented 6 months ago

@oghzzang This is great. Looking forward to your feedback. Thank you!

Best, Suoqin

merckey commented 5 months ago

@oghzzang Hi Oh, I have similar concerns regarding the diameter and center to center distance for the CytAssist. Do you have any updates from 10X?

Thanks, Jin

pratibha-bioinfo commented 2 months ago

Dear @oghzzang,

Any updates? I have also reached out to the 10X genomics team. They said there is indeed a discrepancy between the actual spot size and their marketing material online. Their reply was confusing so would like to know if anyone else was able to get the right spot diameter.

Thanks!