Merging 2 datasets in cryosparcv2


I have 2 datasets of the same sample from 2 different microscopes (both Krios) at the same pixel size (0.85A). What is the best way to combine the 2 datasets?
I had a map at 4.3A resolution from the 1st dataset alone (~100,000 particles) in cryosparc v2. Now I have collected more data with a different grid (~100,000 more particles) on a different Krios. But I am not sure what is the best way to merge the new dataset to the old one. Any help would be greatly appreciated. Thanks.


can anyone help with this problem? I remember reading somewhere that in V 2.9, this issue should receive a solution but I don’t seem to be able to find it.


Hi @ahmad, @ClaudiaKielkopf,
To combine particles from two different collection sessions, please import both sets of movies/micrographs or particles, depending on the stage of processing, using Import Movies or Import Particles respectively, or, if you have already been processing both sets of particles in cryoSPARC separately, you can skip down to the drag and drop instructions.

When combining particles, please ensure that:

  • the box size for both data sets is identical
  • the pixel size is identical to within 4 decimal places

Then, to continue processing with both sets of particles, simply drag and drop the respective particles into a new job (for example, below we are combining particles from two different refinements into a single refinement):

Hope this helps!

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Hej Saara,

thank you for your reply, I realised I need to add some detail on my specific problem.

I currently have movies and particles in two data sets of the same protein in two different projects and would like to set up a workspace in one of the projects (or a new project) where I combine the particles for making a combined 3D model.

(I do see how having all my data in one project would have been beneficial. However, I find it confusing to have too many workspaces in one project. Since in the branch view, I end up clicking on the wrong branch and I end up with jobs in the wrong workspaces…)

I don’t seem to be able to drag drop particles across projects. Is there a way that I don’t know of?
I also tried downloading particle stacks and corrected micrographs. Is there a way to import corrected micrographs?

Thank you,

Can CS2 import CS2 particles? When we point to the CS2 particles it always crashes complaining that the particle metadata is not specified. These are CS2 particles that we’re trying to import into a new CS2 project. Is this possible? Also CS2 complains about the .cs files “unknown file format”…

@ClaudiaKielkopf @istv01
CryoSPARC v2.11, released this past Friday, allows for
1 - Combining particles across projects (by exporting the result group, or exporting the job, and then importing into another project)
2 - Import of CS2 particles (either by exporting the result group containing the particles or exporting a job, followed by import)
3 - Various other data management functions
Please see this detailed tutorial for how to do so:

Hej Saara,
thanks for your message, I was very excited when I saw this in the release email! Thank you for adding these handy features to cryosparc!



I pre-processed my data in Relion and my has particles from two Movie folders (same sample, also same pixel size and box size). When I import the data into cryoSPARC, I think I can use the file (from extraction job in Relion) as my mega path, but how should I use the two Movie folders as my data path? In other words, how should I import the data into cryoSPARC for a further refinement in this case?

Thank you very much.


To make things more clear, I re-extracted my particles and the extraction job wrote out two Movie folders as the particles in the file come from two batch of data. Please see the attached picture for what’s it like.



Hey @bryangxl,

You can use a double asterisk to include multiple folders. For example:

Please let me know if that works!

Hi @stephan,

Thanks for the reply. In my case (see photo in my last thread), I tried XXX/Extract/job/*Movies/*Second_Movies, it did not work. And the error says:

Traceback (most recent call last):
File “cryosparc2_master/cryosparc2_compute/”, line 78, in
File “cryosparc2_compute/jobs/imports/”, line 106, in run_import_particles
assert os.path.isdir(far_blob_path), “Parameter particle_blob_path was set but is not a file or a directory.”
AssertionError: Parameter particle_blob_path was set but is not a file or a directory.



Can you try XXX/Extract/job/*Movies/* instead?

Hi @stephan,

Tried and it failed with the same error. To be clear, The Movies folder and Second_Movies folders are two parallel folders in the same parent folder ‘job’. What I am basically trying to do is to load these two parallel folders simultaneously for your data path (in one directory command line). Hope this can help to clarify the situation.



Slightly different to the situation in here, is it possible to merge two datasets that are different in pixel size. I have data sets that were collected with different magnification resulting in different pixel size. Any suggestions?

@bpsubedi This post from some time ago, but essentially still valid today, may answer your question.