Visualizing and handling DESI 3D data

28 views
Skip to first unread message

Alena Bensussan

unread,
Sep 28, 2023, 5:26:28 PM9/28/23
to Cardinal MSI Help
Hi all,

I collected some data using a DESI Synapt G2-Si with ion mobility capabilities. I was having such a hard time visualizing the imzmL file until I realized that Cardinal is having a difficult time with the drift time values in the z coordinate. 

My questions are:
1) Is there any way to visualize the image using just the x, y coordinates? I think the reason why I am struggling to visualize using just the image3D(mse, ~x*y, mz = 637) command is because there are many x and y coordinate duplicates that correspond to the z axis coordinates. 
2) If there is no way to get around this, is there a way to eliminate the z coordinates and reduce the duplicate x and y coordinates to properly visualize my 2D ion images and extract relevant mass spectra?

Thank you in advance!
Alena

Davide G. Franchina

unread,
Sep 28, 2023, 7:19:20 PM9/28/23
to Cardinal MSI Help
Hi Alena,

I would try setting the z value to NULL:
coord(mse)$z <- NULL
or
subset your object by z values. 

This way you should be able to image 637:
image3D(mse, ~x*y, mz = 637)

I hope this works/helps

Alena Bensussan

unread,
Sep 29, 2023, 9:50:27 AM9/29/23
to Cardinal MSI Help
Hey David!

Thank you for your suggestion! This worked so well, I'm able to visualize my data now. This is the full code that I used:

coord(mse)$z <- NULL
mse1 <- mse[,!duplicated(coord(mse))]
image(mse1, ~x*y, mz=637.2, plusminus=0.2)

I didn't try to subset the data but it may be something I try in the future if I want to access the z coordinates.

Reply all
Reply to author
Forward
0 new messages