Leginon

h1. Summary of MSI applications

All the MSI applications shares the same scheme. They are 5-stage acquisition processes

which include a grid atlas, squares acquisition, holes (called subsquare in MSI-Raster)

acquisition, focusing, and final exposures (Tomography for MSI-Tomography). Target finding at

each stage leads to acquisition at the next stage. Drift management, eucentric height

correction, and autofocusing is also involved. The diagram below shows the flow of control in

MSI. The detailed event bindings involved are for advanced users only and can be found in the

chapter covering creating/editing application at the end of the full manual.

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

The The black arrows shows the flow of the excutation that the node where the arrow starts

from initiate the execution of the node that the arrow is pointed to. The green arrow shows

the control of target shift correction by drift manager. The red,blue, purple, and magenta

frames enclose nodes that processes acquisition, focus, reference and preview targets,

respectively. These nodes sets presets through Presets Manager and moved to their targets

using either Presets Manager or Navigation node. The green frames are nodes for drift

managerment.

The following list is a cursory glance at the steps to run this application:

*  Calibrations (autofocus, image shift, stage position, modeled stage position,

...)

*  Set-up Presets (gr, sq, hl, fa, fc, en, ef)

*  Acquire Corrector images.

*  Acquire a grid atlas.

*  Select squares on the grid atlas. The process can be wholely automated from this

point until more squares are selected.

*  Optionally interact with the hole finders.

*  Optionally putting targets from different images at the same level into queue that

can be processed in a batch.

This chapter has been divided into sections to facilitate everyday usage:

<link linkend="preleg1setup">Pre-MSI Set-up</link>: Prior to setting up Leginon for the

day, make sure that the presets have been designed and Leginon calibrated for your

purpose.

<link linkend="MSI_pref">MSI preference &amp; configuration</link>: The comprehensive MSI

preferences and configuration example.

<link linkend="MISQuickStart">MSI Quick Start checklist</link>: A short check list for

users who are familiar with the application and have saved preferences.

<link linkend="MSISetupDetails">MSI set-up in more details</link>: The more complicated

MSI Leginon application set-up that should be completed before collecting data.

<link linkend="MSIQueue">MSI queuing option</link>: Introduction to the queuing

option.

<link linkend="QExpTarget">MSI Exposure Target queuing</link>: The setup and operation of

queuing mode for large number of exposure targets and/or for avoiding accessing sq presets

after initial acquisition and targeting.

<link linkend="QHoleTarget">MSI Hole Target queuing</link>: The setup and operation of

queuing mode recommanded for quick overall survey of rare hole targets in grid squares.

<link linkend="MSI_troubleshooting">MSI Trouble shooting</link>: This trouble shooting

section addresses some of the possible challenges a Leginon user may face while using the MSI

application.

NOTE: The Tietz imaging software (EMMenu) must be turned OFF before Leginon is started. In

contrast to this, the Gatan imaging software (Digital Micrograph) must be ON before Leginon is

started.