Putting this as a feature request because it doesn’t seem possible at the moment.
I often export particles for processing in standalone cryosparc during a live run. For example, to check for coma through beamtilt refinement or test refinement in different box sizes.
To get the good particles, I need to run 2D classification, even if streaming 2D is ongoing. As far as I know, the only way to use the streaming 2D classification results is to end the job, otherwise a connected select 2D class job says waiting because inputs are not ready.
It would be great for the ability to directly export those particles selected in 2D classification.
Not sure I understand correctly. But if you select classes from a streaming 2d run and then start a streaming ab initio, then cryosparc live will write out a select job (with the particles that are going into ab initio) that you can access from the standard interface. This select job you can then use as input for your refinement tests. Maybe that workaround solves your problem
Just wrote the same suggestion before reading. don’t forget to change number of particles used to very large. Can only be done once, though, per session, so I second the request to “force” selection/export. export currently selected particles (next to export particles and export exposures) would do it.
I would like to get around running extra jobs (save GPU time) or altering my streaming jobs. I want to keep the homogeneous streaming refinement running and not alter the ab initio job leading to it. This way I can run independent tests on subsets of good particles while the streaming refinement does its thing. Running standalone 2D with exported particles can take hours with downsample and needs multiple GPU. The point of live processing is to be fast and inform on data quality, so quickly grabbing the good particle subset is very helpful.
I figured I could use csparc2star to convert the streaming selected particles to a star file for import. But there is no selected_particles.cs file for the streaming 2D?? Am I missing something?
The only files I see available for 2D streaming are:
J1_082_class_averages.cs
J1_082_class_averages.mrc
J1_082_class_averages_noisemodel.npy
J1_082_class_averages_partial.npy
J1_082_particles.cs
J1_082_particles_rejected.cs
I convert the J1_082_particles.cs to star file and import works, but it’s the total particle stack, not just the selected subset.