I have a very large *.im file (>700MB) and my computer does not seem to be able to process it in 'one shot', most likely due to limited memory. Can I process the data in parts, for example by loading only specific masses or specific planes?
Yes, this is possible by following these processing steps.
1:10to load planes from 1 to 10, or
1 2 5:9 20:30to load planes 1, 2, 5 to 9 and 20 to 30.
xyalign.matfile generated in step 5.
In the next stage of processing, you need to generate a preferences file that will contain information required to load all the *.mat files generated in the previous processing stage.
prefs.mat. Note that the folder where you store them should be without the suffix that indicates that only one plane was loaded (_p1-1; see point 5).
Now you are ready for the final stage.
prefs.matyou created in step 7 above. This will load all the accumulated masses stored in the *.mat files.
You can now proceed with data processing in the usual way. That is, auto-scale accumulated images, define ROIs, export ratio images and ratio data in ROIs, make scatter plots, create PDF output, etc. Don't forget to store preferences (in the same
prefs.mat file) at the end of your dataset processing session! This will allow you to use the same settings in the future.
Clearly, once you have loaded accumulated data, you cannot do operations that assume multiple planes, such as plotting depth profiles in ROIs for all masses at once. If you really want to look at depth profiles, though, load the data again in parts and process them as described in steps 1-4 and 9 above. Then, load ROIs from disk using the ROIs menu. Now you can plot depth profiles of (and only of) the selected masses.