I am currently running cryosparc v4.4.1 where when I run 2D classification- I observe considerable amount of Rejected Particles.
Case 1: Particles were imported in a different instance using older version of cryosparc. With the newer version, new instance was created and the project was moved from older to newer instance.
When I used the particles from old extract job (transferred from older instance), the job selected 1million particles and rejected 95k particles and had a message
“Could not find micrograph pixel size in particle’s locations. Will assume particle image pixel size is equal to micrograph pixel size! Note that if particles were downsampled, this will be false, and remove duplicates will use an incorrect distance scale.”
Hence I re-extracted the above (no Fourier crop) in the new instance/new version, which had no rejected particles and no message.
However when I performed 2D classification I had 1.2 million particles rejected only 37k particles are accepted.
Case 2: In the same new instance/new version- I performed a re-extract micrograph after topaz extract. Reject particles here is 0. Upon 2D classification- again there are rejected particles (~ 1/2 of accepted particles). After performing Abintio or 3D classification, whenever I do a 2D- there are rejected particles.
Hence out of curiosity I performed an abinitio of these rejected particles- it gave nice volume.
Can anyone please share if you noticed the same and how to work around it? Thanks for your patience, You deserve a gold medal for making it through this long message