Welcome to pyimzML documentation!

This package provides a parser of imzML format as well as a simple imzML writer.

Typical usage pattern is as follows:

from pyimzml.ImzMLParser import ImzMLParser

p = ImzMLParser('Example.imzML')
my_spectra = []
for idx, (x,y,z) in enumerate(p.coordinates):
    mzs, intensities = p.getspectrum(idx)
    my_spectra.append([mzs, intensities, (x, y, z)])
    # ...

from pyimzml.ImzMLWriter import ImzMLWriter

with ImzMLWriter('output.imzML', polarity='positive') as w:
    for mzs, intensities, coords in my_spectra:
        # writes data to the .ibd file
        w.addSpectrum(mzs, intensities, coords)
# at this point imzML file is written and files are closed

API Reference

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