I apologize in advance if this question has been posted.
I have been running a 3D homogeneous refinement using 376,885 particles as an input. Then, I downloaded the csv file “Result meta data file for iteration 00006” but this one only includes 324,396 particles. I was wondering what happened to the ~52k particles not in the csv file? I guess maybe there statistics are too bad and not included in the reconstruction?
Also, is there a way to actually download the csv file of these particular missing particles?
Where did the input particles come from? If they were selected from an ab initio or heterogeneous refinement experiment, CryoSPARC will by default select the particles corresponding to a class probability threshold of 0.9 - you can change this threshold in the job settings.
If you want to see how many particles were actually used in the refinement, click “show from top” and you should see somewhere in the log that it says something like “300000 particles included at a confidence value of 0.9” - these are the ones that will be used for refinement and included in the output metadata file.
Thanks for the reply. You are right, I missed the fact that the default input_class_thresh is 0.9 even for the refinement. That’s the reason why I see this difference.