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A PyQt interface for mzml2isa parser - imzML edition.


This program is a Graphical User Interface for the mzml2isa parser. It provides an easy-to-use interface to convert mzML files to an ISA-Tab Study. It was made with Python3 and PyQt5.


With PIP

If pip is present on your system (comes along most of Python install / releases), it can be used to install the program and its dependencies:

pip3 install imzml2isa-qt

Without PIP

Once dependencies installed, clone the imzml2isa-qt repository to a folder with writing permissions:

git clone git://

After that, either run the GUI directly:


Or install it locally to run with imzmlisa-qt command:

cd imzml2isa-qt && python3 install


Open the GUI with the imzml2isa-qt command. To simply parse .imzML files to ISA, select the directory containing your files. With default settings, the program will create the new ISA files in that folder, assuming the folder's name is the study identifier (MTBSLxxx for instance for MetaboLights studies). This can be changed by unticking the Export result to directory of each study box. Once parameters are set up, click the Convert button to start the parser.


Generating a study to upload on MetaboLights requires pieces of information the parser cannot guess from the mzML file alone. To provide more metadata to your final ISA-Tab files, use the Add Metadata button to open a new window and update details about your study. Still, even with all the required fields filled, the generated ISA needs to be enhanced after the end of the parsing (using for instance Metabolight pre-packaged ISA Creator to add missing fields).

Missing information required for MetaboLights upload are at the moment: - Study Factors (sample dependent, must be added to the study file

and to the investigation file)
  • Metabolite Assignment Files
  • Study Designs


  • Either add a metabolite assignment file field to main window or change the mzml2isa parser behaviour so that it successfully detects metabolite assignment files and add them to the study file.