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test issues in JEOL
Added by Xing Meng about 10 years ago
Hi Anchi,
The leginon installation on JEOL 3200 seem OK Now (on K2 PC)
We started to do calibrations and met many problems.
After doing dark/bright correction for K2linear and k2counting modes,
k2linear always collect noise images (no structure appeared)
k2counting shows
"can't find references"
When doing presets for lower mag (below 2000)
it failed.
But I tested inside python (import jeolcom; t=jeolcom.Jeol();t.Magnification();); it can read most (low mag)
Replies (3)
RE: test issues in JEOL - Added by Xing Meng about 10 years ago
Anchi,
The beam current reading seems not right
JEOL meter reading 3 PA while leginon is ~e-6
RE: test issues in JEOL - Added by Xing Meng about 10 years ago
Anchi,
Another bug.
Preset assign to TEM will go to a lower step.
For example, preset mag=5000 when assigning to TEM it is 4000
preset mag=40000 assigning TEM shows 30000
Xing
RE: test issues in JEOL - Added by Anchi Cheng about 10 years ago
Regarding beam current reading, you will need to adjust the constants at the beginning of jeolcom.py. Christian got those numbers from his particular microscope. You will need to experiment with them or find the conversion from JEOL for your case. For example, the conversion for current reading (pA) on a JEOL scope to the arbitrary or beam diameter value (meters) is defined in that file as CURRENT_DENSITY_SCALE.
Regarding the magnification, compare the list of low_magnifications and magnifications in jeolcom.py with what is on your scope. When Leginon or any automation program sets magnifications by giving an index number. Since each JEOL model is unique, the magnifications list in jeolcom.py look up the item at that index and then tells Leginon what magnification it is. It is likely that the current list does not match the actual magnifications for the scope.
We can work out the problem with low magnification setting and other problems you have in a remote session.