Leginon

h1. Hitachi 7800 specific installation

h2. Install myami package on the associated camera computer

* Instead of installing myami package on HHT scope-controlling PC, the access can be through the computer controlling the digital camera.

* No special supporting package needed.

h2.hht.cfg

hht.cfg records some instrument specific parameters that are required to convert the instrument output to SI units that Leginon depends on.

The values in pyscope/jeol.cfg.template is based on NYSBC HT7800 equipped with TVIPS XF416.  You may start with these and copy it

to pyscope/jeol.cfg or other [[locate global config directory on Windows|valid myami configuration file locations]].

h2. instruments.cfg

[scope]

class: hitachi.HT7800

cs: 4e-3

* You will also be adding the camera in the same instruments.cfg since this file is located on the camera computer in this instruction.

h2. Testing with pyscope

In python command

<pre>

from pyscope import hitachi

t =hitachi.HT7800()

t.getHighTension()

</pre>

You should get the current gun high tension value in Volts.

h2. Leginon Calibration specifics

h3. Initial [[Setup and Calibration for hht.cfg and focus_offset]]

h3. Follow the general installation and Leginon setup manual until you run "Calibrations" application and finishes obtaining your [[Bright_and_Dark_reference_images]].

h3. Refining scales in hht.cfg

Unfortunately, Leginon's targeting relies on fairly good scale values in hht.cfg.  If you have low confidence on these initial estimate, we recommend doing some iterations of the following:

# Calibrate [[Pixel Size Calibration|pixel size]] more accurately at each magnification used, including lower magnification with the defocus that will be used in experiment.

# Iterate adjustment of COIL_PA_SCALE, COIL_IA_SCALE values in hht.cfg and recalibrate in Leginon.

h3. Image Beam Compensation calibration

Hitachi scopes do not have a high level function we can access through scripting to move image shift without affecting beam location.  Therefore, any Leginon node that uses IMAGE SHIFT move type should be changed to BEAM-IMAGE SHIFT.

This affects calibration procedure in two ways:

* Image Shift should be calibrated at smaller shift distance if the beam moves too much to affect correlation.

* [[Image Beam Compensation Calibration]] at mid and high mags (i.e. mags for hl and fa,fc,en,ef) is required to perform the compensation

h3. Modeled Stage Position calibration

We have observed that HT7800 stage targeting works well only if using modeled stage position as the mover. Follow [[Modeled_Stage_Position_calibration]] to do the calibration.

* Number of periodical terms can be set to 0, and the number of data points in the calibration as few as 5 for it to work. We think the improvement comes from non-orthogonal stage axes that is not accounted for in simple matrix calibration.

h2. [[Leginon Operation  for HT7800]]