[Markus Stoeckli]

I guess it all comes down to get the info on the ProTOF format so that someone can write a converter to Analyze, or even better, the new i-mzML format.

Markus

[Markus Stoeckli]

hmm… It really looks like there are only MSI experts reading this forum with no expertise in MRI… I suggest to directly contact Marting Rausch to get his input on this.

Markus

[Markus Stoeckli]

Based on your observation, I guess that the routine for writing the t2m-file has some flaws. The BioMap import routine would not generate the observed mass shift. This issue is best paced with the team who built the acquisition software.

Markus

[Markus Stoeckli]

Did you try to generate a movie from a window without a ROI overlay? Also, you may want to try different codecs to find out which one works best on you computer. I typically use mpeg…

Markus

[Markus Stoeckli]

Thanks for reporting this shortcoming. We have this dll only in the compiled version and can therefore not make any changes to it. Would you know of a alternative library for exporting movies in IDL? The one we currently use is extremely simple to handle (open file, select encoder, add frames, close file). Something similar for 64 bit would be great.

Markus

[Markus Stoeckli]

There is no unique publication on BioMap. Please reference as "BioMap (Novartis, Basel, Switzerland, http://www.maldi-msi.org)".

Markus

[Markus Stoeckli]

Please try to open the files after moving them to a different directory without special characters (no spaces, no commas) in its name.

Markus

[Markus Stoeckli]

Yes, a proper installer is on the list for BioMap, but I just didn’t get to do it… Anyway, just extract the files from BioMap.zip to the location of your choice. I typically put it under C:\Program Files\BioMap. On some systems you might not have write access to this location, so just select another one of your choice. Go to APPDATA directory (enter "set %appdata%” in the command line to find out where that is) , create in there a folder with the name BioMap and copy all the files from the Setting directory (located in the BioMap program folder) into this folder.
Or replace the install-win.bat file from the distribution with the attached one and run it…

Markus [file name=install_win.bat size=5309]http://www.maldi-msi.org/components/com_joomlaboard/uploaded/files/install_win.zip[/file]

Post edited by: markus, at: 2007/12/06 13:56

Attachments:

• install_win.bat

[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.

Markus

[Markus Stoeckli]

I never used this function and I passed on this question to the person who wrote this routine. You may also want to have a look at [url=http://www.biomap.ch]www.biomap.ch[/url] for MRI related information.

markus

[Markus Stoeckli]

Please have a look a the following example. Biomap handles the image data as floating point variables. Try it out and use Analysis > PixelScan to display the vaules for each pixel.

[img]components/com_joomlaboard/uploaded/images/divide.jpg[/img]

Post edited by: markus, at: 2007/11/16 01:38

Attachments:

• divide.jpg

[Markus Stoeckli]

The nomenclature for divisions in BioMap is somewhat confusing… The active window will be used as numerator. In the division menu, the reference window field selects the denominator. The selected output window will hold the quotient. Please give us a detailed description of your observation (ev. with screenshots) so that we can look into this issue.

Markus

[Markus Stoeckli]

[b]BioMAP 3.7.5.5[/b]

[ul][li]import routine for MSI files allows also importing of incomplete files (as long as the *.hdr and *.t2d are correct)[/li]
[li]problem with missing link from voxel size to geometry matrix solved[/li][/ul]

[Markus Stoeckli]

BioMap does calculate the average of the intensity values in each bin.

markus

[Markus Stoeckli]

Please ensure that you have no dots in the file name or the directory name and let us know if the problem persists.

Markus

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