Does the functions bin_files.extract_spectra and bin_files.calibrate_spectrum exist in the new repository version?

[hillygold]

I am interested to calibrate the spectrum and move from TOF to mass, but many functions that were available in the past under bin_files are missing (bin_files.extract_spectra, bin_files.calibrate_spectrum, bin_files.tof2mass). How can I perform calibration and move to mass?

[srivarra]

Hi @hillygold, thanks for checking out our repos!

I'd suggest instead of using mibi-bin-tools instead we have a pipeline for extraction and post-extraction processing (such as normalization) over in toffy for MIBI-TOF bin files.

[hillygold]

I didn't find in toffy a notebook that does this calibration. Can you explain how can i perform it?
It is different from the normalization.

[ngreenwald]

We don't do calibration as part of our extraction, so you'll need to get those scripts from a previous commit in the repo if you want to run it as part of your workflow.