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StochasticAnalytics / emClarity

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Filament orientation seems to be incorrect in 1.5.3.11 #143

Open bHimes opened 2 years ago

bHimes commented 2 years ago

I am running emClarity 1.5.3.11 and have an issue with the avg step.

I run

emClarity avg param_align.m 0 RawAlignment

My param_aling.m file has the following:

Raw_angleSearch=[45,5,180,5,1]

When I look at the map

cycle000_xxx_class0_REF_ODD.mrc

I looks wrong, the mask is alone Y as it should be but I see a cross section of the filament in the XY place, so it seems the filament long axis is still along Z axis.

Any idea why the average does not come out as intended (aligned on Y axis)?