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.

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.

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.

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.