Hi,
> using a 3D reference generated in Spring
Is it in the correct gray-scale?
Using a reference in a wrong gray-scale is one of the
most common reasons for autopick to perform badly.
> Rather than the HelicalTubeID numbers increasing sequentially, many of
> the HelicalTubeID numbers are skipped. Does this suggest that some
> filaments are 'found' but excluded on the basis of a setting given in
> the job setup (e.g. Minimum length) or something else
Yes. For example, some fragments might be rejected being too close
to the edges of the micrographs.
> Perhaps related to this, what is the relationship between the
> AutopickFigureOfMerit and the Picking threshold value given in the job
> setup (in this case 1.075), that determines which filaments are included
> in the star file? I find a wide range AutopickFigureOfMerit values (also
> negative values) assigned to the included filaments, and it's not clear
> to me what the threshold/deciding factor for inclusion is.
The filament mode has to find tracks instead of points, and there are many
complications here. If you want to study, relevant codes are in
extractHelicalTubes() and exportHelicalTubes() of autopicker.cpp.
> In general the output includes many 'good filaments', but misses what
> appear to be very clear examples regardless of the threshold value used.
Unfortunately, our auto-picker is far from perfect.
This is on our TODO list.
Best regards,
Takanori Nakane
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