{"id":3389,"date":"2019-10-28T16:07:54","date_gmt":"2019-10-28T16:07:54","guid":{"rendered":"http:\/\/apmaldi.com\/main\/?page_id=3389"},"modified":"2023-03-09T16:45:24","modified_gmt":"2023-03-09T16:45:24","slug":"using-mt-imzml-converter","status":"publish","type":"page","link":"https:\/\/www.apmaldi.com\/main\/tutorials\/using-mt-imzml-converter\/","title":{"rendered":"Using MT imzML Converter"},"content":{"rendered":"\n

In order to work with imaging data following software tools\nshould be installed:<\/p>\n\n\n\n

  1. ProteoWizard<\/a> (Windows 64-bit installer (able to convert vendor files) is recommended)<\/li>
  2. MT imzML Converter<\/a> <\/li>
  3. Imzml visualization tool. For demo we are using DataCube Explorer<\/a> <\/li><\/ol>\n\n\n\n

    MT imzML Converter should be configure prior use. Open Settings dialog using File->Settings menu item and configure path to the ProteoWizard msconvert executable (typically located in C:\/Program Files\/ProteoWizard\/ProteoWizard <version> folder). In case of Waters instrument \u201cUse Waters File Dialog\u201d checkbox should be checked. Resample checkbox should be checked on majority of new instrument. <\/p>\n\n\n\n

    Workflow consists of following steps<\/p>\n\n\n\n

    1. Conduct imaging experiment and save both raw\ndata from mass spectrometer and Target Raster XML in the same folder with the\nsame name<\/li>
    2. Run MT imzML Converter and select input raw\nfiles and Target XML file, then press Start button<\/li>
    3. After two step conversion procedure (raw ->\nmzml -> imzml) two imzml files should be generated (one with imzml extension\nand second one with ibd)<\/li>
    4. Visualize imaging experiment with DataCube\nExplorer<\/li><\/ol>\n\n\n\n

      Sample data are available for download here<\/a>.<\/p>\n\n\n\n

      General Information<\/h2>\n\n\n\n