Loading MSI data

[Krista Berlin]

Cardinal Help Team,

I am an R novice and new to Cardinal. I'm having trouble loading my data. I have a Bruker Ultraflex that exported my data as both .imzML and .ibd. When I try to load and open my data file I get this error:

>file <- "c:/Users/krist/Desktop/Test/imzML Data files/MB_9AA_N_08252021.imzML"
> mse <- readMSIData(file)
reading imzML file: 'C:\Users\krist\Desktop\Test\imzML Data files\MB_9AA_N_08252021.imzML'
detected ibd binary type: ‘continuous’
reading ibd file: 'C:\Users\krist\Desktop\Test\imzML Data files\MB_9AA_N_08252021.ibd'
done.

Any help would be greatly appreciated. 

Krista

[educh...@gmail.com]

Hi Krista, 

I can’t see any error. Your code is ok. 

Now you have your acquired tissue in the mse variable.

You can try now to generate an image to see if you have any problem with the file.

Regards,

Edu

[Giulia Ricciardi]

Hi Krista, 

as Edu said, I can' see any error either. Your file looks okay and loaded.

To check if it's loaded correctly and see all the details about the file, run this:

> mse

To visualize the image, you have to choose an m/z value of interest and use this function:

> image(mse, mz=866.459)

I usually add other details like:

> image(mse, mz=866.459, plusminus=0.01, contrast.enhance="suppression")

so I can visualize the image better.

Hope this helps!

PS: Keep going with R! :) I'm a novice too, the improvement is slow but steady and in the end it will be rewarding!

Greetings,

Giulia