From the MSiReader user community, when loading imzML files that are generated using Fleximaging 5.0 or SCILS Lab 2026b (most likely true for other versions), the user needs to make some changes to the Peak Peaking and ROI Spectrum Export default values.
Go to the folder where MSiReader is installed and go to the subfolder "Applications". Open the file "MSiReaderPrefs.ini". Scroll down to the section called "% Peak picking and ROI spectrum export" The default values are too high for Bruker data as they scale their data during generation of the imzML file. Change the values for Peak Threshold and Spectrum Average Threshold to 0.01. Default values are 200 and 100 which will remove most if not all of your peaks during the export.
From the MSiReader user community, when loading imzML files that are generated using Fleximaging 5.0 or SCILS Lab 2026b (most likely true for other versions), the user needs to make some changes to the Peak Peaking and ROI Spectrum Export default values.
Go to the folder where MSiReader is installed and go to the subfolder "Applications". Open the file "MSiReaderPrefs.ini". Scroll down to the section called "% Peak picking and ROI spectrum export" The default values are too high for Bruker data as they scale their data during generation of the imzML file. Change the values for Peak Threshold and Spectrum Average Threshold to 0.01. Default values are 200 and 100 which will remove most if not all of your peaks during the export.
