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horvatovichlab / MSIWarp

MAss spectra alignment tool for MSI data
MIT License
16 stars 5 forks source link

Interface to Cardinal or MALDIquant #3

Closed jipeifeng closed 3 years ago

jipeifeng commented 3 years ago

Hi: Thank you for developing this software. Do you have designed interfaces to software, like Cardinal and MALDIquant. By the way, an example is really appreciated.

Thank you!

Peifeng Ji

j-o-eriksson commented 3 years ago

Hi,

Thank you for your interest!

MSIWarp can be interfaced to Cardinal and MALDIQuant implicitly by loading and saving files in the .imzML format.

There is a complete example notebook of how to align a data set from MetaboLights in the example folder (warp_orbitrap_desi_imzml.ipynb).

The readme file also summarizes how to use MSIWarp together with pyimzML (although with the code to setup alignment parameters is omitted)

I hope those examples can help you! Jonatan