Manual Coma Free
Added by Michael Cianfrocco almost 3 years ago
Hi Anchi,
I'm trying to use leginon for calibrating coma free alignments for aberration corrected beam image shift data collection. I'm following all the instructions fine, but I don't know what to press / change when I get to the Manual Free Coma step (attached). It is displaying the zemlin tableau at x=5um y=0um image shift, but I don't know how to adjust the coma using leginon. What am I missing? I see that when I click on the tableau things change but I don't know if this is how I'm supposed to adjust the coma.
Or do I switch out of leginon to manual coma free alignment using direct alignments?
Thank you!
Mike
Replies (4)
RE: Manual Coma Free - Added by Anchi Cheng almost 3 years ago
The operation of that gui is the same as Beam_Tilt_Imager.
For each image-shifted zenlim tableau gui Leginon presents to you, you want to adjust the beam tilt until it shows as coma-free.
When you click OK, Leginon will save such beam tilt as the correction it needs to make for that image-shift in the calibration. If you Cancel, it will reset back to the value you started with so you can try again
The tableau is displayed in such a way that your current beam tilt (btx, bty) is at the middle, and tilting (by magnitude of d) in each beam tilt coil axis is shown as if in Cartesian system:
top row: (btx,bty+d)
middle row: (btx-d,bty) (btx,bty) (btx+d,bty)
bottom row: (btx,tby-d)
Or if I just write the difference part
top row: (0, +d)
middle row: (-d,0) (0, 0) (+d,0)
bottom row: (0,-d)
The distance between the center of each power spectrum is mapped to beam tilt delta d.
When you use the click tool on the tableau, where you click on will be the beam tilt it will move to as the new center.
In your example screenshot, the spectra on the two side of the center-middle is most dissimilar in the x-axis direction, suggesting that you need to move your btx to the negative x direction but can leave bty the same. If you click half-way between the left-middle(delta of -d,0) and center-middle (0,0), Leginon move the center by (-d/2, 0) and then acquire a new tableau around that point.
I am not sure you will be able to use direct alignment to do this. I suspect that the scope software will reset beam-image shift back to zero before it starts.
RE: Manual Coma Free - Added by Michael Cianfrocco almost 3 years ago
Thank you for your explanation - I had not seen this description for how to use Beam Tilt Imager, which is why I was confused. I appreciate your patience in explaining this me!
Mike
RE: Manual Coma Free - Added by Anchi Cheng almost 3 years ago
You are welcome. Do you think it would be more clear if I put some tick mark to indicate the tilt delta on the tableau image in the documentation ?
RE: Manual Coma Free - Added by Michael Cianfrocco almost 3 years ago
Hi Anchi - after reading your description it makes sense to me. But additional lines like tick marks could help users know that interacting with the tableau helps to adjust beam tilt.