Leginon

h1. Setup and Calibration for jeol.cfg

All setup and calibrations are done on the computer that has access to JEOL's External COM through temext.dll.

h2. Copy from pyscope/jeol.cfg.template to pyscope/jeol.cfg

The current template is based on a JEM-3200FSC

h2. Modify [tem option] section in pyscope/jeol.cfg according to your scope

h3. Using PLA for image shift

Image shift is normally achieved with IS1.  However, PLA is a sometimes a better choice, especially if energy filter is involved.

h3. Lens Series within MAG1 and LOW MAG modes

There are distinct sets of objective and projection lens settings within MAG1 mode that gives

different scale and neutral values.  We assign each of these lens series (LS) numbers, starting at 1 at

the lowest mags. Similarly, we also named the lowest LOWMAG mode lens series LM1 and assign a

different deflector scale to them.

The order of magnifications is therefore roughly

<pre>

LM1->the rest of LOWMAG->LS1->LS2->LS3->the rest of MAG1

</pre>

* To simply the mapping of magnification to the projection modes, MAG1 will be used if a magnification

can be achieved by either LOWMAG and MAG1*

These four configurations like these therefore define the boundary of each lens series within the mode.

<pre>

LS1_MAG_MAX = 5000

LS2_MAG_MAX = 30000

LS3_MAG_MAX = 100000

LM1_MAG_MAX = 200

</pre>

h2. Run pyscope/scalecalibrator.py to get values for different items in jeol.cfg

With the main viewing screen down do these at the computer with EXTTEM3 access.

# Open pyscope/jeol.cfg with a text editor and leave it open so that you can enter values as you go.

# Double click pyscope/scalecalibrator.py to start it.

# The script will first make the scope go through all magnifications in LOWMAG and MAG1 range to determine valid magnifications.

# After choosing tem options, enter the magnifications at which to calibrate.  Make sure that you include at least one magnification in each lens series that you will use.

# Follow the instruction to shift each coil or mechanism by the amount indicated.  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)