Visualizing and handling DESI 3D data

[Alena Bensussan]

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]

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]

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.