[Markus Stoeckli]

I missed that post, please excuse for this late answer. No, there’s no flag. BioMap just checkes for the presence of a file with the same name but the extension ‘.t2m’. The values in there must be in the single precission float format.

markus

[Markus Stoeckli]

Doesn’t Bruker offer some sort of a converter or export filter? Please let us know if you find out…

markus

[Markus Stoeckli]

OK, added two new options based on your comments…

markus

[Markus Stoeckli]

Malcom Clench prov?ded a demo image which was acquired by his student Sally Atkinson on a Q-Star. Many thanks!

The data can now be downloaded from [url]http://www.maldi-msi.org/download/demo.zip[/url].

net-climber

[Markus Stoeckli]

I think there is a fairly simple solution to this problem. In the ‘Instrument Settings’ of the ‘Control Panel’ you must disable the ‘Automatic Voltage Shutdown’. This is typically set to 30 minutes and then the voltage is switched off – for this reason the top half of the images remains black.

markus

[Markus Stoeckli]

To answer this question we need the input from our MRI specialist – who is currently in the Himalaya. He’ll be back soon…

markus

[Markus Stoeckli]

We have to live with this limitation for the moment. There is something in the works… no promise, though. Should things change, I’ll post it in this forum. 😉

markus

[Markus Stoeckli]

[b]BioMap 3.7.2[/b]

New Features:
[ul]
[li]functions for peak analysis (max, peak shift)
[li]new icons
[/ul]
[i]To upgrade from a previous version, simply replace all the files in the BioMap program directory with the files of the full version. Make sure that the license file is not deleted.[/i]

[Markus Stoeckli]

Du musst in Tools/Geometry/Exchange SLice Evolution gehen. Der letzte Index ist immer der des Parameters und der muss gr?sser 1 sein. Wichtig ist auch noch, dass man mit Edit/Header den Parameter-Array mit den entsprechenden ADC-Werten auff?llt.

[Markus Stoeckli]

How do you define the term ‘smoothing’? For displaying our images, we often use the interpolate function, as show in the example below:

[img]http://www.maldi-msi.org/components/com_joomlaboard/uploaded/images/raw.jpg[/img]
raw pixels

[img]http://www.maldi-msi.org/components/com_joomlaboard/uploaded/images/interpolate.jpg[/img]
interpolated

Is this by your definition also a form of smoothing which one should not apply to images?

[i]In BioMap, one can switch between the two modes by right-clicking on the window, clicking on Properties and selecting the DisplayMethods in the Display tab[/i]

markus

Post edited by: net-climber, at: 2007/01/08 20:16

Attachments:

• interpolate.jpg

[Markus Stoeckli]

We found some bugs in BioMap 3.7.0 running under MAC OS and fixed them in the official release 3.7.1.

markus

[Markus Stoeckli]

[b]BioMap 3.7.1[/b]

New Features:
[ul]
[li] support for MAC OS [i](many thanks to Rich Knochenmuss who let me test and debug the software on his G5 MAC OS X system)[/i]
[li] project manager
[li] windows batch file and shell script for installation
[/ul]
Bugfixes:
[ul]
[li] minor bugs
[/ul]

[Markus Stoeckli]

OK, here we go: [url]http://msi.stoeckli.net/download/BioMap370.zip[/url]. BioMap 3.7.0 is still beta, but it should work on MAC OS X. Please reports bugs to this thread.

Markus

[Markus Stoeckli]

Could you gives us more information on the effect you observe? You define the image coordinates by moving the plate in the 4700 so that the laser fires at the edge and then you transfer this positions into the imaging tool by the buttons provided?

How big is the difference between the defined image edge and the actual image border? Does it appear to be a systematic error or is it unpredictable?

One thing which I consider as a source for this behavior is the plate calibration. Did you image a calibrated plate?

markus

[Markus Stoeckli]

Do you also get the message ‘The BioMap main path might not be set correctly’ upon startup of BioMap? If so, the settings files were not copied to the default location. For a Windows installation, execute ‘Install settings.bat’ located in the BioMap program folder and the default settings will be copied.

markus

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