Leginon

h1. Creating Presets for the first time

Configuring the Presets are critical to many different applications. Presets describe

camera configurations such as image size and exposure time as well as many other microscope

parameters such as magnification and defocus. Setting presets in calibration application is

optional but recommended for determining what calibrations are needed for future runs.

h2. Design Presets

MSI presets can be customized to your need of data collection. By matching

nodes/subnodes in MSI with presets and move types, the behavior of the node is

defined.

See the section on [[Pre-MSI Set-up|Designing Presets]] in the chapter

for MSI application for more explanations on the presets standardized at NRAMM which we will

reference in this chapter, we use here the nomenclatures at NRAMM that is used to collect

defocus paired images with four scales of targeting ant two sequences of focusing using an

MSI application. You will need to adjust the preset parameters for your own camera, scope,

as well as the grid mesh you use.

h2. Presets Created for Convenience in Calibration

The table shows an example of the presets for an MSI application. For calibration

purpose, undefined image shift can be left as what recieved from the scope. Beam intensity,

spot size, and should be adjusted to give reasonable signal to noise ratio for usable

exposure time and for the beam to cover the whole CCD. The exact setting of exposure time

can be set later after bright and dark images are collected.

|_.Magnification:|_.Preset name:|_.Image Shift (x,y):|_.Binning:|_.Dimension:|_.Beam Coverage:|_.Exposure Time (ms):|_.Spot Size:|_.Defocus (m):|

|120|gr|as is*|8|512|max|20|4|0.0|

|550|sq|as is*|4|1024|1x CCD size|100|4|-2e-3|

|5000|hl|as is*|8|512|1x CCD|20|4|-1.5e-4|

|50000|fc|0,0|1|512|<~ 1x CCD|300|4|-2e-6|

|50000|fa|0,0|4|1024|>2x CCD|50|4|-2e-6|

|50000|en|0,0|1|4096|2x CCD|170 (10e/A^2)|4|-1e-6|

|50000|ef|0,0|1|4096|2x CCD|170 (10e/A^2)|4|-2e-6|

* Use whatever image shift from the microscope when the preset is newly created. These

will be aligned later.

h2. Create Presets from microscope setting

*  (Optional) Microscope/Reset defocus at eucentric height.

*  Adjust the microscope settings at the microscope. This includes magnification,

beam intensity, beam shift, and defocus. Beam intensity and beam shift is adjusted to

get the good beam coverage shown in the table. Defocus only need to be

approximate.

*  Leginon/Node Selector>Select "Presets Manager" node.

*  Leginon/Presets Manager> Click New From Scope icon !http://emg.nysbc.org/software/leginon/images/icons/instrumentgetnew.png! to open "Create New Preset" setting window.

*  Leginon/Presets Manager/Create New Preset> Type a descriptive name for a

Preset, "hl" for example, left-click "Create" to save and close the window.

*  Leginon/Presets Manager/Preset Parameters/Camera Configuration> Change the

image shift, defocus, camera configuration and exposure time if necessary. It will be

saved automatically when changed.

h2. Presets Selector and Cycle Order List

If Presets are not ordered as in the table above, we recommend that they are rearranged

for efficient cycling. Cycling is important for minimizing hysteresis effect on em optics

and targeting and are defaulted to be on in Presets Manager Settings. To reduce cycling

time, it is best to group the presets that often occur consecutively in order. For example,

the typical MSI preset order as in the table above.

*  Leginon/Presets Manager> select a preset from the Preset Selector.

*  Up/Down: Move the presets up or down in the Cycle Order.

h2. Adjusting Presets at the microscope

With cycling activated as default, the preset beam shift may behave differently from

that was first created. The following procedure check, adjust, and save the presets

parameters with cycling accounted for.

*  Leginon/Presets Manager> select a preset from the Preset Selector.

*  Leginon/Presets Manager> click To Scope icon !http://emg.nysbc.org/software/leginon/images/icons/instrumentset.png! to send the current preset to the microscope.

*  Adjust the microscope settings either at the microscope or in a node that

controls the microscope (Instrument) and/or the camera (Navigation,etc.).

*  Leginon/Presets Manager> click From Scope icon !http://emg.nysbc.org/software/leginon/images/icons/instrumentget.png! to save the current settings to this preset.

h2. Using Presets in Calibrations

With presets created, calibrations at different magnifications can be changed by sending

the corresponding preset to the scope.

*  Leginon/Presets Manager> select a preset from the Preset Selector.

*  Leginon/Presets Manager> click To Scope icon to send the current preset to the

microscope.

h2. Calibration Status

Calibration status of a preset is displayed in PresetsManager right below the message

log panel. This section is very useful for troubleshooting calibration problems. Over time,

certain calibrations may need to be repeated. This section will display the latest

calibration date related to the current preset.

Check this section to see which calibrations the new preset will need to be

completed.

*  Pixel Size: This value is entered through the Pixel Size Calibrator node.

(required)

*  Image Shift: This is calculated through the Image Shift matrix calibration.

(required)

*  Stage: This is calculated through the Stage Shift matrix calibration. (Optional

if Modeled Stage Mag Only calibraion exists at the same mag).

*  Beam Shift: This is calculated through the Beam Shift matrix calibration

(Optional; Necessary to move the beam in Navigator).

*  Modeled Stage: This is calculated through the Modeled Stage Position calibration

(necessary to accurately center holes/targets for high magnification images).

*  Modeled Stage Mag Only: Same function as in 5. This may be created from full or

mag only model fit in GonioModeling.

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[[Startup Calibrations|< Startup]] | [[Pixel Size Calibration|Pixel Size Calibration >]]

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