MSI-T exposure targeting/acquisition
Added by Cheri Hampton almost 14 years ago
Hi, we are setting up the MSI-T node. We are stuck at the acquisition stage. Blobs worked. We couldn't get lattice to work, but were not concerned because we only got one blob of the two present. We have played with the ice thickness threshold settings and run test, but don't get anything. This is without the focus template or the target template checked. We've tried plugging in different numbers for ice thickness threshold. Is there some other non-transparent factor we need to consider?
Replies (6)
RE: MSI-T exposure targeting/acquisition - Added by Anchi Cheng almost 14 years ago
Try take the curser hover over the "lattice" target displayed on top of the image, you should be able to see stats for the target, then you can use the number there to guide your acquisition settings. If still not sure what to do, you may want to send us one of such images (in mrc format so that the intensity values are preserved) so that we may try it.
RE: MSI-T exposure targeting/acquisition - Added by Cheri Hampton almost 14 years ago
Do you mean the button over the image?
RE: MSI-T exposure targeting/acquisition - Added by Anchi Cheng almost 14 years ago
More specifically, the one labeled 42. See graphical_User_Interface in the section for Image_Viewing
Also see Hole_Targeting_Set-up_for_MSI-T under heading 5._Leginon/Hole_Targeting/Lattice> for an example of what you should see.
RE: MSI-T exposure targeting/acquisition - Added by Cheri Hampton almost 14 years ago
This is exactly as we were trying to do. Here is this image.
RE: MSI-T exposure targeting/acquisition - Added by Anchi Cheng almost 14 years ago
I let mine find Max. Blobs = 1 (Leginon will pick the one closest to the center which means your goniometer need to behave reasonably well.
Lattice fitting becomes irrelevant for one blob input. This gives me one lattice target.
I then set Hole Statistics settings: Radius= 50, reference intensity = 12000 (12000 is a guess, empty hole should be brighter than the hole.
The hole stats turns out to be Mean Intensity~9990, Mean Ice thickness~0.18, S.D intensity~744, S.D Ice thickness ~0.077. With these information, I can then get acquisition/focus targeting.
Hope this helps.
| targeting.png (461 KB) targeting.png |
RE: MSI-T exposure targeting/acquisition - Added by Cheri Hampton almost 14 years ago
Yes, it certainly did!