merge two datasets collected at different magnifications


Dear All,

We have two datasets for which data has been collected at different magnifications. Now, we want to merge stacks from both the datasets.

I have query to how to introduce more than one stack with different pixel size in mparameter file. We are using frealign_v9.11.

Your help will be highly appreciated.

Thanks and Regards

Frealign can read in several datasets and combine them in a reconstruction. However, this function is not supported by the user-friendly scripts. You should read the README.txt file and maybe also look at the old script examples that are still available on the Frealign download page. Alternatively, you reconstruct both datasets separately and add the 3D maps afterwards to get a better overall map. The get maps that have the same pixel size (so that they can be added), make sure that the pixel size in mparameters is set to the same value for both reconstructions, dstep is set to the correct detector pixel size and the magnification values in the Frealign parameter file are correctly set to the calibrated magnification at the detector.

In reply to by niko

Dear Niko,

I'm processing 2 datasets separately using frealign.
Now I'd like to combine these 2 and am wondering how I can do it more efficiently?
Is it possible to combine the par file and do a final refinement at the very last?
If I combine the datasets and run frealign again from beginning , could it be possible to achieve better reconstruction compared to combine last par file, and then do the final refinement?

Thanks a lot,

In reply to by claire89

If all the microscope settings are the same, the two stacks and parameter files can be combined into one. In the parameter file, make sure that the particle number (the first number on each line in the parameter file) counts up continuously from 1 in the combined parameter file.