Eucentric focus off when queing exposure targets
Added by Bob Grassucci over 9 years ago
Hi Anchi
I have a user using Leginon and queueing the exposure targets but when MSI-T sends en or fa to the scope it is about 20 microns from the true eucentric focus. Any idea why it does not hold the correct value?
I tried setting defocus to -1 microns then -2 manually rather than using random within range to see whether defocus calibration was off but that seems fine. When it goes to focus it sends the wrong obj lens value to the scope and it is off by about 20 microns.
When I manually put the objective lens values to eucentric focus and save the value from the scope when it is in Fa preset it seems to hold temporarily. I think the problem reoccurs when the queue is submitted. Could that be?
Thanks,
Bob
Replies (2)
RE: Eucentric focus off when queing exposure targets - Added by Anchi Cheng over 9 years ago
HI, Bob,
Sending presets to scope changes defocus, which is a relative value, while eucentric focus saved from scope saves the absolute objective lens value.
I am not aware of any place in Leginon that sets directly objective lens value and resets defocus there, the situation that would give the behavior you observed. It is slightly possible though that retrieving a queued parent imaging condition for target adjustment may have changed defocus value, but it should not reset defocus to that point. Hence, the next preset sent to the scope will not be affected by it.
Eucentric focus value saved in Leginon database does have magnification dependency. On the other hand, defocus value only depends on lens program or so-called projection system mode, giving different zero point in SA/M vs LM mode.
All these explanation probably does not help you, though. I have two things that you can do and see if it gives better diagnosis:
1. Record the objective lens value during this process. You can either refresh the instrument panel in "Scope" node (on your scope Leginon Client), It would be under Focus/Focus. Or copy it off TUI. The reason for wanting to check this is in case that it is sending the right value but appears to be at different focus due to hysteresis of the lens.
2. This and other information like this is in the database. If you get me a database dump, I might find something there.
What is your Leginon version right now ? I can check to see if there are recent changes that may explain this.
Anchi
RE: Eucentric focus off when queing exposure targets - Added by Bob Grassucci over 9 years ago
We are using version MSI-T2 3.0
This defocus problem only happens when we are queuing exposure targets according to the user. Another user is currently on the scope so I will try the diagnosis you suggest when I get a chance. Until then no one is queuing.
Bob