align presets with each other: black images between hl and ex but normal images between hl and sq
Added by Zhiheng Yu almost 11 years ago
Hi Anchi,
We have set up Leginon on a Titan Krios with a K2 camera. All the calibrations were done and checked to work well. We experienced a puzzling problem while aligning presets to each other. When aligning "sq" with respect to "hl" both images were obtained properly (see the attached screenshot). But when aligning "hl" with respect to "ex" or aligning "gr" with respect to "sq", black images show up. In the preset manager node, I have tried both 1024 and 512 for the "small image size" setting. The results were the same. The above observations were made using "full camera" mode. If "similar look across mags" were enabled, in the "ex"-"hl" pair the "hl" image shows up while the "ex" remains black. There were no problems at all to take images at each preset separately. The problem only occurs when align presets to each other.
The details for each presets are:
ex -- SA 14000x, Gatan K2 counted, 3710x3838 bin1, 1000ms;
hl -- SA 1700x, Gatan K2 counted, 927x959 bin4, 500ms;
sq -- LM 205x, Gatan K2 counted, 927x959 bin4, 500ms;
gr -- LM 50x, Gatan K2 counted, 927x959 bin4, 50ms;
Thank you very much,
Zhiheng
Replies (2)
RE: align presets with each other: black images between hl and ex but normal images between hl and sq - Added by Anchi Cheng almost 11 years ago
The lens normalization occurs when magnification changed may be too long for the tool which was originally made to take images as fast as it could.
There is a settings in "Presets Manager" accessible in the toolbar "Presets Manager/Settings" called "Apply pause time in the preset alignment tool". Activate that and try to adjust the pause time between preset changes.
It does not quite explain why you could get hl image when using "similar look across mags". It is possible that the additional image processing needed for this digital zoom in the "hl" image was just enough to allow acquisition when beam is returned.
RE: align presets with each other: black images between hl and ex but normal images between hl and sq - Added by Zhiheng Yu almost 11 years ago
adding a 1 second pause time fixed the problem. Thank you very much,
Zhiheng