[Markus Stoeckli]

If the t2m file contains valid data, the size should be 4 times the size of the data dimension, since the m/z values are stored as single precission floats.

markus

[Markus Stoeckli]

We are still working on the full imzML implementation for BioMap and currently there is only [url=download/BioMap3801Update.zip]this version[/url] available as a beta software. I expect the work to be finished by December this year.

markus

[Markus Stoeckli]

Hmm, either you start by getting a hands-on training or you hire a postdoc from a known MS imaging lab to support you… You may check this site for upcoming trainings. The next potential date is August 30, 2010.

Markus

[Markus Stoeckli]

No, there is no free software for imaging on the QSTAR. We use the oMALDI Server software from AB SCIEX on the QSTAR Elite, but I don’t know if this will work on the pulsar.

Markus

[Markus Stoeckli]

This statement is based on my experience and can be challenged. Please use this forum to discuss MSI related aspects instead of PM.

[Markus Stoeckli]

This is caused by UAC in Windows 7. Run the installation script with Administrator privilege and it will work. Alternatively, you may edit the uparsrc file located at C:\User\\Application Data\BioMap.

[Markus Stoeckli]

Oh, I somehow missed this post….

You may save the default layout in the setting, but it is not possible to set the default color table and scripting is also not implemented in BioMap. But these are things to put on the wish list for a new version or software…

[Markus Stoeckli]

imzML is still not fully implemented and there is currently only a beta version available for download.

[Markus Stoeckli]

Which data format do you try to import? If it is imzML, this might be caused by the a newer file type than the one implemented.

[Markus Stoeckli]

MS images are typically generated from peak areas and smoothing will not enhance the result if you have many data points over the peak.

[Markus Stoeckli]

The following message was received from Akos:

Dear Peter,

Few days ago I could manage to install BioMap on my Mac (OS X 10.5) and it works fine ever since. I think the trouble is the licenserc file that seems to best in the biomap system directory (/.biomap).

I installed the BioMap into my user directory and modified the uparsrc-linux-mac file also in the /.biomap directory.
Now, my question is how familiar you are with the Mac OS structure (I was not for sure) to be able to find hidden directories and files? The reason is that ALL system directories and files are hidden by default on Macs and there is no simple switch to show and hide them like on PCs in the Folder options. When I realized this I made two plug-ins with the Automator following the description on this site:
http://theappleblog.com/2007/04/30/quick-tip-showhide-hidden-files/
Then I could easily find the biomap system dir (/.biomap) and copy the licenserc file into it.

However, it still did not work for me for the reason that the licenserc file was not correct!
First I got the message from the Webmaster without any attachment only written the code as text that looked like this:

TYPE =3D 13571
ID =3D 725341
EXP =3D 108075823
MRI =3D 0
MSI =3D 67388375
WIP =3

Following discussion with Markus he pinpointed that this is not a correct content of a licenserc file and suggested to remove all “3D”s. At this point I have to add that I created this file with TextEdit and removed its extension. So, it became like this:

TYPE = 13571
ID = 725341
EXP = 108075823
MRI = 0
MSI = 67388375
WIP = 0

After that it still did not work however.
Then I got the idea to apply for the code again. This time I got the file as attachment as well but to my surprise it looked differently opened by TextEdit (first line was empty!):

âÌzCz…TYPE = 13571
ID = 725341
EXP = 108075823
MRI =
MSI = 67388375
WIP =

And it did not work but it did after the first (empty) and the garbage in the second line was removed!!!

In conclusion, my recommendation is to play around with the licenserc file and get it in right format and BioMap will run nicely on Mac.

Good luck!

Akos

[Markus Stoeckli]

If you have a 3d data set (3 spatial and 1 spectral dimension), you may use this view to browse the data.

Markus

[Markus Stoeckli]

Did you also try to copy the file to the user dir, in your case C:\Users\Mic\AppData\Roaming?

[Markus Stoeckli]

The img file structure is descibed in this forum, please use the search function and you’ll find it. But… you may want to start writing software for the new imzML format. Its a XML format, making live much easier…

Markus

[Markus Stoeckli]

The only thing which is new in this version is a modifiaction to the installation script. If you already have 3.7.5.5 on your system, stay with it. We tested BioMap with IDL 7.0 and it worked without problems. The next version will support i-mzML… please contact me if you want to test our current beta version…

[Author]

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