After Inspect picks, it is clearly picking some particles, and it seems to me that the ones it is missing are those with the highest contrast. Perhaps there are some automatic exclusions based on the local power that are being applied behind the scenes, which are appropriate for cryo but not for negative stain? This is with the upper power threshold set to the maximum value:
Hi @apunjani, to me it seems to be an issue of some kind of contrast threshold, not a missing negative sign - because it is correctly picking some of the particles, just missing those with the highest contrast, as far as I can tell. Whereas if I import NS data as cryo, it picks around the particles and doesn’t pick any negatively stained particles at all.