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K2 image and movie rotation and flip
Added by Aguang Dai almost 7 years ago
Hi there,
To make the image from GMS (DM) exactly as that in flucam (LM and SA), I rotated K2 270degre and also flipped.
It's a standalone K2.
In dmsem.cfg, I also make sure "FLIP = True" and Rotation as 3 (90 degree * 3).
After dark and bright reference correction, I did image shift matrix calculation.
It succeeded (at least no error message), however when I double-checked in Navigation model, when I clicked on a target,
it moved to the opposite position rather than the target.
I'm wondering what other setup needs to be done.
Thanks.
I have never seen Leginon with this problem. A new calibration should be all it needs.
If you have preset for your calibration settings, please check in Presets Manager if the date of the calibration corressponds to your new work.
If it does, we may have to do a remote session so that I can watch the behavior.
Hi Anchi,
Thanks for the help.
I made some mistake in Navigation, that's why it seems "image shift matrix" failed.
Now image shift is OK.
But we do have a gain reference correction or K2 rotation/flipping issue, and that's why I'm changing the rotation and the flipping.
Basically, when I use GMS to collect a movie and do frame alignment in GMS, the background looks right (no weird strip feature).
But when we collected movie using leginon and did frame alignment in GMS (the same position and beam setting),
we always saw weird feature (some strip feature) in the background.
We tried turning off "correct image" in exposure, the background feature is still there, no matter in empty area or with feature.
As I mentioned before, I make sure in "dmsem.cfg" file, it's "FLIP = True" and "Rotation = 3" because that's the setting in GMS.
Do you happen to have experience with this phenomenon or have a clue where it goes wrong?
We're thinking either "dmsem.cfg" in our K2 PC might not work and somehow the gain correction in our setup doesn't work correctly.
Thanks.
Best,
Aguang
Hi, Aguang,
We have never used Leginon to collect movie and then do frame alignment in GMS. We have always done it outside with MotionCor2 and programs like that. There is a flip in the frames (non-gain-corrected) due to a differences in convention between programs. Therefore, if you take what is saved by Leginon (or more correctly, by SerialEMCCD.dll) and put into GMS and apply GMS gain, it will be flipped upside down.
Turning off "correct image" in exposure does two things:
1. The sum image that you see in Leginon gui will not have gain correction. You should see growth zone in there. Like what I show in K2_gain_correction.
2. Leginon database will not associate the image/movie frames with a gain reference recorded in Leginon (called norm image in our documentation).
It does not affect how the frame movie is saved. The frame movie will always be non-gain corrected because it is more efficient in compression later.
If you wonder whether your dmsem.cfg is correct, check image tree in the image report in your webviewer. See Common_Features on how to get there.
Your configuration is most likely result in what is shown in this snap shot. frame_flip=1 corresponds to what I said earlier.
