When a particle is very elongated, cryosparc severely clips the highlights in the output 2D classes (only for those classes looking down the long axis of the particle). In the thumbnails in the job card, the highlights are handled correctly.
Would it be possible to alter the output such that no highlights are clipped? I want to make nice pictures of 2D classes for a publication, and unfortunately once highlights are clipped, there is no way to recover lost detail.
Happy to provide examples offline if needed.
The highlight clipping is intentional to deal with the cases where there are some junk classes that have very strong positive/negative values (e.g. carbon edges). In those cases using the min and max value of all classes as the black/white levels means that all the real classes get washed out. We also wanted to make sure all classes are shown on the same black/white level inside the job so they can be compared. So currently we use a percentile (I think 5 and 95 percent) which can clip highlights that shouldnt be clipped sometimes.
In this case probably the best way to make publication figures would be to generate them separately using the .mrc 2D template outputs of the 2D class job? We’re hoping to eventually add more interactive visualization tools like this.
we can do that, but it is genuinely annoying for asymmetric particles - top views routinely get clipped and lack detail
maybe going to 1 and 99 might fix this?