Leginon

h1. Queuing Example 3 - Both Exposure and Hole Targeting

MSI-Tomography application is an example of such queuing set up. It is also the useful

when energy filter is used. It is chosen so that the microscope stays at the same presets as

long as possible to obtain all the images so that LM preset sq will not need to be used once

tomography data collection starts.

h2. Configuration

*  /Square/Toolbar/Setup/Wait for a node to process image = no

The "no" setting saves time by acquiring images while holefinder and YOU are picking

targets.

*  /Hole Targeting/Toolbar/Setup/Queue up targets=yes.

*  /Hole Targeting/Toolbar/Setup/Allow user verification of the selected targets=yes,

if desired.

*  /Hole/Toolbar/Setup/Wait for a node to process image = no.

*  /Exposure Targeting/Toolbar/Setup/Queue up targets=yes.

*  /Exposure Targeting/Toolbar/Setup/Allow user verification of the selected

targets=yes, if desired.

h2. Operation

*  Select square targets on grid atlas and submit as usual.

*  All sq images will be acquired while "Hole Targeting" finds the targets on each sq

image since waiting in "Square" node is off. Note that since the square node acquires

images continuously, both hole finding and acquisition may compete for processing and

memory time. If it affects your interaction with the program, just wait for the

acquisition to complete.

*  If you have just acquired many (such as 50) sq images in LM mode, the microscope

has stayed in LM for a long time. It is advisable to set the instrument to one of the

preset in HM mode as soon as the acquisitions are completed and check for possible image

shift inconsistency between presets. If energy filter need to be on for higher

magnification imaging, do so now.

*  If user verification is turned on in "Hole Targeting", the targets should be

submitted using "submit"<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/play.png" format="PNG"/>

tool.

*  The Queue is submitted and processed only when "Submit Queued Target"<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/send_queue_out.png"

format="PNG"/> tool is clicked.

*  Repeat the same target selection and submission process at "Exposure Targeting"

node.

*  In case when leginon crashes during queue processing, the data acquisition should

be resumed by "Submit Queued Target"<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/send_queue_out.png"

format="PNG"/> in "Exposure Targeting" node first. If nothing happens, it means the

queue in that node is empty. In that case, repeat it in "Hole Targeting" to

resume.

h2. Interruption

Once the queue is submitted there are several modes of interruption

*  If leginon crashes during queue processing, the data queue acquisition can be

resumed by "Submit Queued Target" in first the "Exposure Targeting Q" node, then if

nothing happens, in the "Hole Targeting" node.

*  Queued targets from "Hole Targeting" can be paused in "Hole" node with "pause"

button and is <link linkend="MSI_pause">recommanded for the liquid nitrogen refill of

the side-entry cryo stage</link>.

*  The "Abort" button<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/stop.png" format="PNG"/>

in "Hole" node aborts the acquisition of the remaining targets from the same parent "hl"

image and proceeds to process targets from next square in the queue.

*  The "Abort Queue" button<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/stop_queue.png"

format="PNG"/> in "Hole" node aborts all remaining targets in the queue.

*  Exposure targets are paused and aborted in a way similar to the queued Hole

Targets.

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[[Queuing Example 2 - Hole Targeting only|< Queuing Example 2 - Hole Targeting only]] | [[Monitor Progress of Queued Targets|Monitor Progress of Queued Targets >]]

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