Hole centering on K3

[Willem Noteborn]

Hey Jonathan,

We are currently testing smartscope on our main Krios system equipped with K3. We see that during hole centering (ptolemey) the rectangular K3 image gets cropped into a square of which is actually the right side of the K3 instead of in the middle. The hole then gets centered in that square and afterwards the full rectangular image is taken again. This causes the hole always to be off center (always off to the right). Is there any way to force the cropping (if necessary at all) to be in the middle of the detector? It makes the hole selector miss most shots.

Best,

Willem

[Jonathan Bouvette]

Hi Willem,

Thanks for the feedback. It's not something we observed on our krios-k3 system but I'll go over the code and try to see what is wrong.

Best

Jonathan 

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[Jonathan Bouvette]

Hello again,

I'm quite uncertain about this one. The only crop command in the SmartScope code is CropCenterToSize which should automatically be centered.

Here a summary of how the ptolemy centering works:

1- on the first square, acquisition, a View image is taken to create a hole reference for the grid

2- All full holes found on that image are cropped out and averaged to create the template image which gets saved in buffer T

3- on each subsequent hole acquisition, the View is acquired, then cropped to the size of the reference

4- The cropped image is aligned to the reference

The cropping is not necessary but we found it to be better at avoiding aligning to a hole too far from the center of the image. There is no good way to disable the behavior without going into the code and removing the line.

First, I would try running a `CropCenterToSize A 512 512` from the script window just to see how it behaves in SerialEM alone.

Then, I'd like to know which mag you are using for View. Do you see at least 9 holes? We usually use the lowest SA mag available.

You may want to look at the reference image in buffer T. Does it look ok? The image should remain there after stopping smartscope until overwritten.

Finally, which version of SmartScope and SerialEM are you running?

Best,

Jonathan

[Willem Noteborn]

Hey Jonathan,

The CropCenterToSzie gave proper centered cropping. I was using EPU type of settings logic for the view mag, as there you absolutely don't want too many holes in the view as it will confuse the software which hole to take (so very much one hole per view types of magnification). But I guess overcoming this problem is taken care of in your software by the cropping as you mentioned. After following your suggestion to just use the lowest SA mag it now centers fine! So that seems to do the trick nicely.

Thanks for the quick response!

Willem

Op maandag 4 september 2023 om 03:16:45 UTC+2 schreef jonathan...@gmail.com:

[Jonathan Bouvette]

Yes, the goal of the cropping is to narrow it down to one hole close to the center while providing a medium mag image with information about the surrounding holes.

I'm glad that it's now working!

Best,

Jonathan