Summary of MSI applications » History » Revision 2
Revision 1 (Amber Herold, 04/22/2010 05:00 PM) → Revision 2/7 (Amber Herold, 04/27/2010 11:35 AM)
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 & 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. ______ [[Flavors of MSI applications|< Flavors of MSI applications]] | [[Pre-MSI Set-up|Pre-MSI Set-up >]] ______