Front Page Forums BioMap Export from Fleximaging Re: Export from Fleximaging

Markus Stoeckli

1) Once you open a file, select Analysis > Plot > Point to show a spectrum for each image point. Then, either drag your mouse with the right mouse key pressed over the spectrum to select the molecular image of interest or use the middle mouse button to mark a peak of interest to calculate the corresponding molecular image.

2) This software was not written for Windows only but for multiple OS and does therefore not use the Windows registry. Once BioMap is open, go the Edit > Defaults menu and point the BioMap path to the location where you installed BioMap to.

3) (response to Arne) Nobody claimed BioMap to be user friendly, but once properly installed, it does offer some unique features. The correct handling of geometry information is one of them. When you import an MSI file into BioMap, the voxel size is also loaded (I don’t know if the Bruker software does actually write it into the file). Go to Edit > Header and select the Coregistration tab. Check if for the correct voxel size (in mm) or change it to you actual acquisition resolution. When you import an optical image, do the same (e.g. 300 dpi results in a voxel size of 0.085). If image areas are the same, you can directly overlay them. If not, use Tools > Geometry > Coregister to shift and rotate the images till they match.