Is anyone aware of a way of normalising peak intensities in Biomap ? We find it useful to normalise images to a matrix ion intensity (usually m/z190 for aCHCA) in each pixel across the whole data set. 😳 ‘scuse mistake in first version of this post
Open your MSI and extract one image with your reference mass (e.g. matrix peak or a compound added to the matrix). Use ‘Tools-Calculation-Divide’ for normalizing the whole data set with your reference image.
Is there a way to normalise against the total ion count for each pixel using Biomap? I have tried selecting the whole spectrum using the middle mouse bottun, but the ion intensities displayed do not reflect the total ion count for each pixel.
If you select the mean (not mean with BC) value over the whole mass range, you’ll end up with an image containing the mean value for each pixel. Your intensities will be low, but you can rescale the image and redefine the range (menu tools-intensity) so that you have a scale ranging from 0 to 1.
I tried to slected one image window (m/z 190 for CHCA) as reference to divide other windows(other m/z) in a scan. But I found the resulted window didn’t change much compare with original one. But the resulted CHCA window (m/z 190) is more confusing. After normalized by itself, a uniform image is expected. But the resulted image is still similar with the original window (before normalization). Need help. Thanks
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.
Thanks for the reply. It does clarify some confusions. But it still doesn’t solve the problem. Since the intersted peak is stronger than the reference peak (such as matrix peak) in some location of image, the quotient will then be larger than 1. However the output window only display from 0 to 1. And those area (relative intensity higher than 1) will be display as dark area (low density area). How can I adjuste it?
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.
Is there a way by which I can compare a normalized image and a non-normalized image in BioMap? To see how better is the new image from the previous one.
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