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.

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 & 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.

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< Flavors of MSI applications | Pre-MSI Set-up >

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