Leginon

h1. Pausing and Aborting during data collection

Users may need to pause leginon data collection when filling cryo-stage and cold trap or

making adjustment to image or beam shift of a preset or even perform certain microscopy

alignment. Pausing is possible when leginon is waiting for user input at target finder level.

Alternatively, pausing can be made in any acquisition node with the pause tool.

The pause tool (as well as the abort tool), when clicked, does not interrupt acquisition

until the next possible point that is at the end of an acquisition sequence for a target. When

the play tool is clicked at a later point of time, leginon should move the stage and image

shift to that defined by the next image. Here are some examples of the valid pausing

points

*  At the end of an acquisition sequence for a target in the middle of a target list

that may also be one of the queued list.

*  At the end of an acquisition sequence for a target at the end of a target list that

may also be one of the queued list.

*  Before a focus target is repeated after DriftManager is done monitoring drift.

Currently, you can not pause at the following points:

*  Within the preset list of an acquisition target

*  Before any target is processed at the node

h2. Pausing in MSI application

For those using MSI-type of application, we recommand the following pausing

point:

Case 1: Exposure Targets are NOT queued

*  At Hole or Subsquare (MSI-Raster) node, click on the "Pause" tool any time and it

will pause before the start of next hole in the same square.

Case 2: Exposure Targets are queued

*  In Exposure node and click on the "Pause" tool while the last target is being

acquired. Leginon will then pause at the end of the exposure sequence.