Leginon

1. LS refers to lens series. If there is only one projection lens, the strength of the projection lens used is scaled directly according to the magnification. We can just scale the magnitude of the deflector values by the magnification ratio if we want to know how to deflect the beam by a fixed physical amount at a different magnification. In today's EM, multiple projection lenses are used, there are multiple combinations sets (LS) that adjust the strength used on each to produce the effect of a given magnification with minimal rotation of that projection image. As a result, We observed that it is not always straight forward in scaling the deflector values. Whenever we run into a situation in where the deflection has jumped to a different value. especially in rotation, when we increase magnification to the next inder, it means the scope has switched to a different LS.

It was how JEM3200 and JEM2100 behaved. It is possible that CryoARM LS transition is more smooth now so you won't have to define many LS. First do it according to Mode available to you. Add more LS divisions within it if it turns out to be necessary.

2. On JEM series as well as many other microscopes, when you do fine adjustment of a knob, it is not an analog increment, but a step-wise change. You might feel a jump in tension when you hold the knob. That "click" is the minimal unit of a digital control. That digital signal unit is what is used in JEOL API so any movement we do needs to be converted to number of "click"s
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3. Aperture size values depend on your microscope installation. When the engineer installs the apertures in the aperture strip, he/she should know what are in there. These values are mainly for display in the TEM Remote node to match. The actual setting is by index in the CLA_SIZES list. For example, 50e-6 aperture in your example would have an index of 3. Size 0 means the open position.

I hope these explainaion helps.

Thanks. That helps a lot.
Another question is how to acquire the scale values and the natural values for beam tilt? I noticed from the example jeol.cfg file that the natural values vary a lot from module to module (e.g., natural beam shift values and natural beam tilt values are different, and even for same module, x and y axis can be distinct values). Where do those values come from? Any clues on finding those values according to the microscope or TEM interface?
For beam shift/image shift, can we adopt similar method to acquire their associated scale and natural values as well?

Leginon issues command to move a deflector in the same physical unit ( meters for distance, radians for angle) regardless of microscope manufactures. jeolcom.py in pyscope uses jeol.cfg to convert that instruction to what JEOL scopes understand in clicks.

This is why the scale value for beam tilt is very different from image shift. As to why x and y axis be different, that depends on the configuration. Ideally they should be similar, but we do know cases that they are different, probably due to construction not orthogonal. Some of the difference can indeed found on TEM interface, but I can not recall the exact interface you need to look into since it has been a while since I last used a JEOL scope.

Yes, the beam shift/images scale calibration is done similar to what is done for beam tilt, just in imaging mode rather than diffraction mode. scalecalibrator.py will guide you through it.

Thanks for explanation. We have been working on scalecalibrator.py and when we run into "Move CLA1 by 1.0 cm on Main Screen in x direction", we were not sure about whether we indeed moved 1cm as requested. Our recorded images before and after adjusting the beam shift are in the attached picture, in which two windows correspond to two images (before and after adjusting the CLA1 y value), and it looks like the two images have a displacement of approximately 1cm, but we don't know if this is correct.
What does the 1cm refer to? Could you explain "The distance between the major ticks of the linear scale bar on the main viewing screen corresponds to 1 cm at the film camera (i.e., nominal magnification)" in more detail?

Thanks for the screen shot. Witth CryoArm only has digital live-view camera, we do have to change the way we do this calibration. The older model all have a window on which the nominal mag is defined. With a physical object, a move of a physical unit like 1 cm makes sense, and thus our base for calibration. This is not true on a digital screen because users are free to zoom-in and zoom-out. All distance has to be measured relative to the scale bar shown. Let me think of how to expose this properly for you.

On the physical viewing screen there is a linear ruler printed on it. The values i was referring to was based on that. JEOL made that so the major tick on that ruler was equal to 1 cm distance at their camera plane. Very useful for reading scale if you know the magnification at the camera.

Thank you. That is a lot of information. We will try working on this procedure using the ruler on the upper viewing screen, and may consult you again for guidance if more questions arise.