we are happily running cryosparc live. However every now and then there happen to be bad images and sometimes they are completely black. This is certainly coming from the microscope. However when cryosparc live processes these images it gets for the motion values 10^38. which screws up the visualisation and the selection and if there is just one image I cant really use the treshold to get rid of them and it also doesnt accept typed values.
Anything that could be done?
Hi @david.haselbach ,
If you would like to reject one or more exposures individually, you can do this without thresholds by manually rejecting them. You can toggle manual rejection of an exposure via the exposure menu or keyboard shortcut ‘r’:
Manually rejected exposures will be excluded from further processing.
Unfortunately there’s no way to hide these outliers on the scatter plots within the overview tab. You can always zoom into the plot to inspect values in detail.
We’ve implemented an update to the overview thresholds to allow any threshold value in the number inputs. This will be released in the next version of cryoSPARC.
Hi thanks for the advice. The main issue we are having is that I cant set any thresholds anymore as it only accepts very high (1e+38 etc) values as thresholds. It doesnt accept when I type other values.
Any chance one can change this?
There is automated outlier rejection for local power for more or less exactly this reason (see Ali’s comment here:Inspect particle picks rejecting high contrast particles [Bug] - #8 by apunjani) - maybe the same is needed for the other metrics to prevent this behavior?
Thanks! But I suppose the problem is even worse here as the outlier I get is super extreme its 1e38 and the reasonable values are in the range around 10
right so should be even easier to exclude on the back end, in the same way as is done for contrast/power