Spot diameter of 10X visium

[oghzzang]

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]

@oghzzang You can check the information here

[oghzzang]

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]

@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]

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]

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

Best,
Suoqin

[merckey]

@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]

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!

[pnolabs]

Dear @sqjin,
Unfortunately, the link you posted no longer works. I am therefore asking again:

Why is the spot size in the tutorial 65 μm when 10X states that, for Visium V1 and V2, it is 55 μm?

Setting spot.size to 55 min(d.spatial[d.spatial!=0]) does not produce a result as close to 100 as 65 does.

Can you help me understand the consequences when sticking to 10X 55 μm diameter for the cellchat anaylsis of Visium v2 data?

Thank you for your expertise!
Cheers, pnolabs

[sqjin]

@pnolabs The theoretical spot diameter is indeed 65um that we confirmed with the help center from 10X Genomics. Please check the related text "In this example, the estimated pixel size was calculated from the spot diameter for the full resolution image:" in the following website:

https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs