Manual picker clips highlights of denoised micrographs


When I input denoised micrographs into Manual Picker, it seems like the highlights and shadows are pretty severely clipped (see example below).

I suspect that cryosparc is automatically thresholding the top/bottom 5% of intensity values, which makes sense normally, to increase contrast, but not for denoised images, which have intrinsically higher contrast. Playing with the contrast intensity override does not help. Would it be possible to add an option to turn this behavior off?

It would also be helpful, when inputting denoised images, if one could toggle between denoised and original while picking, as denoising sometimes gives artefacts near the edges of micrographs.

An image from the same denoised set is shown as viewed in relion_display, so you can see the highlight clipping is not intrinsic to the denoised images.

This gets even more pronounced for micrographs that have sparser than normal particle distribution, which makes me think that it is some kind of auto-contrast routine that doesn’t behave well on denoised mics:

A fix for this phenomenon is included in release 3.3.2


Hi @wtempel, just tested this, it seems that there is definitely more latitude to tweak the settings via the “Contrast Intensity Override” slider, which is great.

One thing I would suggest is making these settings persistent for an active job. Currently if I undisplay and then redisplay the job, the slider resets itself, which is annoying as these parameters can require a bit of tweaking to get just right.


Hi @wtempel,

I don’t think this fix made it into the updated Manual Picker in v4 - the clipping of highlights and shadows in denoised micrographs is back, and the contrast-intensity override slider is gone.

Would it be possible to add this fix back to the new version?