Leginon

h1. Importance of making calibrations

Leginon will not function if calibrations have not been done. In essence, this (or a

similar combination of nodes) is the first application that should be used if calibrations do

not already exist. The term calibrations is an inclusive term that refers to different sets of

measurements such as image shift and stage position.

Unless you plan to perform calibration to all available magnification and camera

configuration, the first step in performing calibration will be to <link

linkend="presets_create">set up Presets</link>.

The following lists all the calibrations that must be completed for Leginon MSI

application to function correctly. Some calibrations can not be performed without existing

calibration of the others. Therefore, it is necessary to follow the order listed below for the

very first calibration for an empty database:

* <link linkend="pixelsize_cal">Pixel Size calibration</link> (for all the magnifications

that will be used)

* <link linkend="cor">Bright and Dark image references</link> (for all the image dimension

and binning that will be used)

*  (Optional) <link linkend="mcal_bm_sh">Beam Shift Matrix calibration</link> (for all

the magnifications that will be used)

* <link linkend="mcal_im_sh">Image Shift Matrix calibration</link> (for all the

magnifications that will be used)

* <link linkend="mcal_st_pos">Stage Position Matrix calibration</link> (for the

magnifications that will be used for gr preset in MSI... e.g. 120x)

* <link linkend="gonmodeler">Modeled Stage Postion calibration</link> (for magnifications

in the range of ~550x to 1100x that will be used for sq preset in MSI...e.g.

550x)

* <link linkend="btcal_def">Beam Tilt Defocus calibrations</link> (for the magnifications

focus will be corrected at, both for z and defocus correction. These are the hl and fa

presets in MSI, respectively... e.g. 5000x and 50kx)

* <link linkend="btcal_stg">Beam Tilt Stigmator calibrations</link> (for the

magnifications where the focus and astigmatism will be corrected at. These are the hl

and fa presets in MSI... e.g. 5000x, 50kx)

* <link linkend="eucenfoc_store">Store eucentric focus value</link> (for the

magnifications where the stage z will be used for defocus correction. The hl presets in

MSI is typical... e.g. 5000x)

* <link linkend="r_center_store">Store rotation center beam tilt value</link> (for the

autofocus magnifications where the image shift is useded as move type in targeting if

the stage is to be tilted. For example, the "fa" preset in MSI... e.g. 50000x)

* <link linkend="dosecal">Dose (camera sensitivity) calibration</link> (for one

magnification, the rest are scaled by the program automatically).

!http://emg.nysbc.org/software/leginon/images/images/Cal_flow.png!

In most cases, calibration only need to be done once. Through experience, we have found

the Stage Position and Calibrations involving Beam Tilt need to be refined often. The other

calibrations (in our experience) do not fluctuate as frequently as these two do. Modeled stage

position calibration does gradually go off over several months and a full calibration of the

modeled stage position matrix is required to rectify the problem.

Image Shift, Stage Position, and Modeled Stage Position matrix calibration are being

completed so that targets can be accurated centered in the images at each different

magnification. At the lowest magnifications, an image shift is too big without inducing

significant beam shift so the stage has to be moved. As the magnification increases, a simple

calibration of stage movement (error typically of 1.5 um or more) is not adequate, so we have

to model the stage movement (error typically of 1 um or less), but still move the stage. At

even higher magnifications (e.g. hl, en, ef, fc, and fa) image shifts (error of 0.3 um or

less) can be used to go to targets.

The following are magnifications and types of positioning calibrations that typically have

been completed at a very minimum:

|_.Magnification:|_.Calibrations:|

|120 (i..e., mag for "gr" preset)|modeled stage position(mag-only), image shift|

|550 (i.e., mag for "sq" preset)|modeled stage position(full), image shift|

|5000 (i.e., mag for "hl" preset)|image shift|

|50000 (i,e, mag for "fa","fc","en" and "ef" presets)|image shift|

The Presets Manager has a "Calibration Status" section that will show which calibrations

have been completed for the given mag the selected preset is set to. We usually calibrate for

a range of magnifications so that later we will not have to complete them.