Stage shift ?
Added by Jean-Paul Armache over 9 years ago
Hi,
I'm occasionally having an issue with the scope/leginon. I am operating Polara microscope with leginon installed. After selecting all the targets, I submit it for collection. Occasionally, I have to pause the app to refill the microscope with nitrogen. Sometimes, the selected targets after resuming are waay off. I use ancestor image and declare drift between images, but it hasn't helped me. I reset the image shift on the microscope side, it also never helped. I figured out how to make it work, by pausing Exposure and resetting the stage in XY (Reset XY) on the scope. Then, when resumed, it works like the shift never happened.
To this end, I was wondering whether you've ever experienced this ? Before the solution, I checked the reported positions on the initially picked and then collected images and their location was identical.
Please let me know,
Best,
Jean-Paul
Replies (2)
RE: Stage shift ? - Added by Anchi Cheng over 9 years ago
Hi, Jean-Paul,
When I set up your scopes for Leginon data collection, I learned that the plan is to use navigator iterative stage shift to get to the target for the final exposure. To save time, it is possible that it was then set not to make target adjustment even if drift is declared since those are not necessary if navigator iterative move is used since it does self-adjust. Is this how you use it ? It will help me investigate the possible cause if you can give me the move types and movers in "Exposure" and "Hole" node.
I have not considered the situation of refill drift like what you said, though, for navigator stage shift. You seem to be doing all the right things in trying to get back the targeting for drifted image. The only one I know that would never help is to reset the image shift on the microscope side since Leginon will send the whole set of the scope parameters over.
If the ancestor is used to make target adjustment, you should notice that after you unpause, it takes an image in "Target Adjustment" node in the ancestor preset (likely 'hl' preset in your case). In that process, the stage would move, and likely giving the same effect as reset XY. You would also get an ancestor image name as a new version. i.e. xxxxhl_v01.mrc saved in the database, and show up in the viewer. Did you get that ? If not, adjustment probably never taken place.
If you have the newer version ancestor images, check where it adjusts the targets to in the web image viewers. Are they correct ? If the new version ancestor images are completely off, it will not be able to adjust target properly, that would be a bad situation, then.
RE: Stage shift ? - Added by Jean-Paul Armache over 9 years ago
Hi Anchi,
I will check it all out and let you know.
Thank you,
Best,
Jean-Paul