Stripes in 3D refinement result
I am working on a scaled and merged dataset, when running 3D refinement, I see stripes across the backgroup (image attached). I used relion scaling one particle set (300keV) from 1.06 A/pix to 1.17 A/pix and merge it with another 1.17 A/pix particle set (200keV), then imported to cisTEM. I did not see such stripes in 2D classification results, but only 3D refinement. Any parameter I should adjust? Thanks!
The particles do have a
The particles do have a preferred orientation, but I did not see such issue when processing individual dataset, it only happened after I merged them. The particles I used are picked after 2D, I think very bright/dark pixels should be aligned there if exist. Also the particles do not contain area outside micrograph. I am wondering if it has something to do with the relion_image_handler command I used in rescaling and reboxing the particles, will check the edge pixels and maybe rebox it into a smaller size and check 3D result again.
282k particles, the stripes
282k particles, the stripes start to show in round 3 and get worse in later rounds. I used default settings for the percentage and threshold, so it is possible in round 3 fewer particles are used in alignment, but the same issue did not happen before I merge the particle sets.
Qi
Sorry, I am not able to share
Sorry, I am not able to share the data, will look into the particle set and post the cause if spot it. Thanks!
Qi
This looks a bit strange.
This looks a bit strange. Does your dataset have a strongly preferred orientation, or are there some very bright/dark pixels in some of the images? Sometimes, when picking with Relion, particles near the edge of a micrograph contain "empty" pixels with values that are not set to a sensible value. Have you checked that particle boxes are completely contained in the micrographs, or that areas outside micrographs are filled with sensible values?