Automate .imzml extraction using timsconvert package

[alex-l-kong]

Is your feature request related to a problem? Please describe.

Currently, the extraction of .imzml files is dependent on uploading to SCiLs, which may take several hours for large .d files. Using the timsconvert package, we can optimize this process up to 5x.

Describe the solution you'd like

Programmatically, timsconvert runs as a CLI tool:

timsconvert --input "{path to .d dir}" --compression="none"

We can use the subprocess library in Python to mimic this call.

Describe alternatives you've considered

Stick with SCiLs. This is becoming too much of a burden.

Additional context

This tool unfortunately does not run on Mac. Users will need to TeamViewer into the MALDI/MALDI-processor computers to run this. Fortunately, we can easily get those repos set up on those computers so people don't have to mount the NAS folders locally. Unfortunately, this extraction will still be limited to the MALDI/MALDI-processor computers themselves.

The MALDI notebook is becoming bloated, we should strongly consider splitting this up. At the very least, separate notebooks for extraction and analysis (not unlike ark-analysis).