In addition to nanoSIMS images, I have imaged the same field of view (FOV) also with another instrument (e.g., fluorescence microscope, AFM, SEM, TEM). I would like to analyze the nanosims and external image data together in LANS. Specifically, I would like to align them, overlay them, extract lateral profiles, define ROIs based on the external image, calculate ion count ratios in these ROIs, plot scatter plots of nanosims vs. external data, etc.
ext. This means that you can use it as such in LANS processing actions.
Here we will describe, by means of an example, how to work in LANS with an external image data generated by AFM. We will use unpublished data kindly provided by Lydia Pohl, TU Munich, and assume that the nanosims images look like this
while the external data look like this
Specifically, we will describe how to
1.0e9(as suggested by default).
*.matfiles, which you can find in the
matfolder as a result of your previous processing of the nanoSIMS data. Note that this image should be chosen such that it best resembles the external image. In this way a good alignment, which you are going to work on next, will be possible. After these steps, the alignment GUI should look similar to this one.
matfolder under the filename
AFM_aligned.mat. By selecting the
*.matoutput format we specify that we do care about the actual values in the external image. Clearly, this is because in our case the values correspond to the height of the surface in nano-meters.
MAT files (*.mat)and select the file created in the first stage (in this example the file
AFM_aligned.mat). Read the message that pops up and click OK.
ext. This means that you can use it as such in LANS processing actions, such as for defining ROIs, calculating ratios, displaying lateral profiles or scatter plot, etc. (see below).
cancelwhen prompted for the external image file in the file selection dialog that pops up. Again, a message should pop up, this time notifying you that the external image is no longer available.
Knowing that the imported external image behaves in LANS as any other mass image (secondary ion counts image), you can make a number of analyses where the data from the external image is combined with the nanosims data. Here are a few examples.
scalefields in the main LANS GUI. If you want to change this scaling you need to close the 3D overlay GUI, change the scale, and repeat point 1.
extin the ROI definition template text field in the main LANS GUI.
One way to identify the relationship between the data in the external image and the nanosims data is by plotting a scatter plot of values averaged over ROIs. In this example, we will check for a relationship between the ratio 27Al16O/16O and the surface height (derived from the data in the external AFM image) in ROIs that look as shown below. All steps are done through the main LANS GUI.
ext/pixel. The reason to normalize the values in the external image by
pixelsis to make it possible to calculate for each ROI the average height of the pixels in the ROI. Note that this normalization is quite essential, as without it the displayed values would be the height accumulated over all pixels in the ROI, which is obviously not what we want to study in this example
G/yfields in the main LANS GUI, check the
Plot x-y-z graphcheckbox, and select Output → Display ratios from the main LANS menu. You will obtain a scatter plot similar to this one.
Another way to identify the relationship between the data in the external image and the nanosims data is by overlaying lateral profiles. In this example, we will check for a relationship between the ion counts 27Al16O and 12C14N and the surface height (derived from the data in the external AFM image).
extin the list of masses below this check box, and click on Display lateral profiles. This will draw an overlay between the selected ion counts and the height as a function of the distance along the profile (see below, right figure). Note that in this overlay the values are normalized such that the range defined by the minimum and maximum values for each displayed variable is mapped to 0 and 1, respectively. The minimum and maximum values are taken from the respective
scaletext fields in the the main LANS GUI.