Queuing Example 2 - Hole Targeting only¶

Queuing in "Hole Targeting" is useful when rare objects can be identified at "sq" preset
and a quick survey of the grid is desirable before acquiring images at higher mags. An example
for such a situation is for data acquisition of 2D crystals.

Configuration¶

• /Square/Toolbar/Setup/Wait for a node to process image = yes or no

yes: Pro-won't cause problem if you forget to change this when you decide not to use
queuing later. Con-time wasted while holefinder is picking targets.

no: Pro-saves some time by acquiring images while holefinder and YOU are picking
targets. Con-if you forget to switch it back on when you decide not to use queue later,
many things can go wrong, starting from nodes competing for the microscope

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

"Declare drift when queue is submitted" is not necessay because Z focus, which is
the first targets for each square parent image will cause a drift declare of its
own.

• /Hole/Toolbar/Setup/Wait for a node to process image = yes (as in MSI depth-first
  mode).

• /Exposure Targeting/Toolbar/Setup/Queue up targets=no (as in MSI depth-first
  mode).

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 if 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 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.

• Since queuing is not turned on at "Hole" and "Exposure Targeting" in this case, the
  data acquisition is ordered as in depth-first mode so that the exposure/focus targets on
  a hole are acquired before the next hole.

• 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 "Hole Targeting" node.

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 "Hole Targeting" node.

• Exposure targets are paused and aborted as usual.

• Queued targets 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.

• If you want to pause queue processing and switch to depth-first mode temporarily,
  and then continue the queue processing, do the following:

• "Pause"<inlinegraphic
  fileref="http://emg.nysbc.org/software/leginon/images/icons/pause.png"
  format="PNG"/> the queue in "Hole" node or "Exposure" node.

• Quit leginon once the program is standby in the paused mode.

• Restart leginon and the application.

• Change configuration to that of non-queuing mode and operate as such.

• When ready to continue queue processing, configure the related nodes as such
  when leginon is idle.

• Click on "Submit Queued Target"<inlinegraphic
  fileref="http://emg.nysbc.org/software/leginon/images/icons/send_queue_out.png"
  format="PNG"/> icon in "Hole Targeting".

• Since Z focus is performed as the first target in the queue from individual square
  and there is no more z reverting for other holes in the square, you can rescue bad
  U-centric height adjustment during "Hole" and "Exposure" acquisition as in the full
  depth-first mode.

---

< Queuing Example 1 - Exposure Targeting | Queuing Example 3 - Both Exposure and Hole Targeting >

---