In order to work with imaging data following software tools should be installed:
- ProteoWizard (Windows 64-bit installer (able to convert vendor files) is recommended)
- MT imzML Converter
- Imzml visualization tool. For demo we are using DataCube Explorer
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 “Use Waters File Dialog” checkbox should be checked. Resample checkbox should be checked on majority of new instrument.
Workflow consists of following steps
- Conduct imaging experiment and save both raw data from mass spectrometer and Target Raster XML in the same folder with the same name
- Run MT imzML Converter and select input raw files and Target XML file, then press Start button
- After two step conversion procedure (raw -> mzml -> imzml) two imzml files should be generated (one with imzml extension and second one with ibd)
- Visualize imaging experiment with DataCube Explorer
Sample data are available for download here.