Concept code for Analytical Chemistry
Convert imzML format to .mat file with the imzml2mat.py script from the Conversion_tools folder.
- Python 3.5, 3.7 and 3.8 are tested.
- Put the script in the folder containing imzML file or files to convert and run the script.
- numpy, scipy, tkinter and ImzMLParser are required.
There is also xml2mat.py Python script in the Conversion_tools folder, which allows conversion generated .xml files of peaklists from old instruments that don't support the imzML format to .mat file.
- Launch CSMM.mat file.
- Load .mat file or press Esc for loading previous file (this is an option to change some parameters in code and work with previosly selected file for not to select the file again).
- Click on any point of the opened Figure 1 iteratively. For exiting the process click the space right to the colorbar or terminate the process (e.g. Ctrl+C in command line).
- Set m/z range, m/z bin width, path to histology image if possible, gaussian convolution and storing the data for figures of CSMM to be saved after each click.