Stitch images side by side

[Maya Najam]

Hi, 

I am looking to combine imaging mass spec files but want to stitch the images side by side. I have tried using the cbind() function but noticed that when I conduct imaging using image() the pixels of both images seem to be superimposed onto one another. Can I instead stitch the two brain cross sections for example together side by side to form a side by side image of both brains. 

Thanks,

Maya

[Andreas Abildskov]

Hi Maya

Are you by any chance using one of the newer models of Bruker instruments (e.g., timsTOF fleX, rapifleX) that requires you to export imzML files from SCiLS? It seems to be a shared problem for other people using Cardinal. It was suggested by another use to use another converter. 

Best wishes,

Andreas 

[Hannah Lusk]

Maya, 

A member of my lab developed a converter for timsTOF fleX data called TIMSCONVERT. I used this converter, and do not have the same problem when using the cbind function in cardinal. 

Paper: https://academic.oup.com/bioinformatics/article-abstract/38/16/4046/6618521

GitHub: https://github.com/gtluu/timsconvert

To make the data compatible with cardinal, you will need to use the command line version (instructions for download and use are on GitHub). Put the file path then "—compression none —verbose —chunk_size 100". 

Hope this helps, 

Hannah

[Maya Najam]

Hi Andreas and Hannah, 

Thank you so much for the resource! I do realize that the imzML conversion is the issue here. We are using a SCIEX TOF device and are looking for ways to convert our .hdr, .t2m, and/or .img files to the imzML format. Do you have any converters that you have found to be helpful for these file types? 

Any suggestions would be greatly appreciated. 

Thanks,

Maya

[Davide G. Franchina]

Hi all,

please see https://github.com/kuwisdelu/Cardinal/issues/24

for a temporary solution to cbind().