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