Dr,wabdelmoula,
We have encountered some problems regarding this part of the data extraction. Can you provide more details on this part()?Thank you very much!
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You can convert the imzML to hdf5 using the following steps:
first install the python packages “h5py” and "imzML"
Load the imzML file to get:
a- spectral data, and let's say save it in a variable called "Spec_Data",
b- spatial information for each spectrum and save it "XCoord" and "YCoord".
use the hhdf5 method called "create_dataset" to save your data in h5. For example:
myHF = h5py.file("myData.h5",'w')
myHF.create_dataset('Data', data=Spec_Data)
myHF. create_dataset('xLocation', data=XCoord)
After you finish, close your h5 file: "myHF.close()"
”“”
Dr,wabdelmoula, We have encountered some problems regarding this part of the data extraction. Can you provide more details on this part()?Thank you very much! “”“ You can convert the imzML to hdf5 using the following steps: