[Markus Stoeckli]

If you registered through the link provided by Bruker BioSpin, the license does not activate the MSI functionality. You may get separate MSI key from this site and combine the keys in one file.

Markus

[Markus Stoeckli]

You can export the data (e.g. as picture) and use a third party software to generate the contour graph. Or if you have the full version of IDL, you may directly access the data from BioMap and within seconds you have a 3D plot. See the BioMap manual for instructions.

Markus

[Markus Stoeckli]

And here is the file Liam was referring to…

[file name=MSI_MIAPE.pptx size=80054]http://www.maldi-msi.org/images/fbfiles/files/MSI_MIAPE.pptx[/file]

Attachments:

• MSI_MIAPE.pptx

[Markus Stoeckli]

There are no known issues with Windows 7 32 or 64 bit. As knelson pointed out, BioMap is somewhat picky about the directory names. Best to stay with the basics, no special characters. And should you run into an issue, please report it back here on this forum.

Markus

[Markus Stoeckli]

[b]ramisir wrote:[/b]
[quote]So, number of data points can be reduced but the intensity issue is still there. Thats what they think![/quote]

And they are wrong…:laugh:

[Markus Stoeckli]

Old versions of BioMap were limited to 16-bit signed values. The actual version supports multiple data types. Check [url=http://www.maldi-msi.org/index.php?option=com_fireboard&Itemid=53&func=view&catid=2&id=13#625]this post[/url] for more detail. Please pass this link on to Prosolia.

[Markus Stoeckli]

[b]ramisir wrote:[/b]
[quote]I am using X-Calibur (version 2.1.0 1139) from thermo. The instrument is Orbitrap XL and I am doing DESI imaging! My BioMap is also 3.8.0.3.[/quote]

Hmm, I’m not familiar with the Thermo imaging implementation. I suggest that you contact Kerstin Strupat at Thermo in Bremen. She’s an expert in MS imaging on their instruments. Please let us know what you find out…

Markus

[Markus Stoeckli]

[b]ramisir wrote:[/b]
[quote]What I am woried about is that in that 4 pixels which I chose, my ion of interest had an ion intensity of 32767! I am sure thats not the real intensity of my ion.[/quote]

Yes, there is an issue, but in the data file and not in BioMap. What instrument and software (version) do you use to acquire your data?

[Markus Stoeckli]

[b]dodge wrote:[/b]
[quote]I also did some testing using dummy data (see excel to analyze topic by markus for more details) in img form. The displayed average in the ROI panel is correct.[/quote]

I’m relieved, thanks B)

[Markus Stoeckli]

[b]ramisir wrote:[/b]
[quote]So you guys think that the intensities from ROI regions CAN be used as a base for quantification as they are not cut or scaled?[/quote]
I would hope so, as we did many studies using this function…

OK, here’s what I just tested with BioMap 3.8.0.3: I loaded an image with intensities above 1E6. I right-clicked on the image and selected Properties. In there, I switched Display Mode to Voxel and then clicked on Done. Then I clicked on the Zoom button and selected an area where I could easily identify 4 distinct pixels. Exit of zoom-mode with right-clicking and Done. With Analysis-PixelScan I got the values of the 4 pixels. Once done, I draw a region over these 4 pixels and looked at the ROI Statistics. The displayed “Mean” value was exactly the average of the 4 pixels. So this seems to work fine. Please describe in detail what you were testing.

Markus

[Markus Stoeckli]

[b]dodge wrote:[/b]
[quote]…intensities are stored as single precision floating point…ROI data is averaged…[/quote]

Thanks, I can confirm this. Markus

[Markus Stoeckli]

There is no direct way to achieve this. You may export the image as picture and use other software to covert a picture to Excel. Or you way save the image as a Scan (“File” – “Scan+”) in Analyze format and then write a small VB program to import this data in Excel. Or, if you have a full version of IDL you may directly use an IDL function to access the image data.

[Markus Stoeckli]

The area is calculated with the number of pixels and their size. Depending on the mass spec data, the pixel (or better voxel) size is directly imported from the data file. If this is not the case, change it in “Edit Header” – “Coregistration”.

[Markus Stoeckli]

[b]knelson wrote:[/b]
[quote]Specifically, I was trying to baseline correct the entire image, and normalize the image, which creates an output image to a new window.[/quote]
Typically we would do in my lab normalizations and BC on extracted images, not the full data set. This is much faster and does not require a significant amout of memory.

[Markus Stoeckli]

[quote]Does anyone know how can I get a list for ion intensities of different ROIs in BioMap that can be exported to excel?[/quote]
For this, select “Roi” – “Statistics” and in there, select “File” – “Export” – “List”. The generated text file can directly be imported in Excel.

[quote]I am not sure how can I get a list that says what do I have in each pixel?[/quote]
This is the same as exporting an images. You may do this in Analyze format or bmp.

[quote]That way I can remove empty pixles from the data set.[/quote]
There is a function to remove “empty” pixels from ROIs in BioMap. Once you have drawn the ROIs, set the Min and Max intensity sliders to the intensity range you want to include. By selecting the grey color scale with blue on the low end and red on the top end one can easily select the matching values. Then select “Roi” – “Clip” and the pixels outside the selected intensity ranges will be removed from the ROIs. Redo the ROI statistics.

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