Resuming an acquisition

Restarting a stopped acquisition

It is possible to resume an acquisition that stopped for whatever reason. The following steps can be performed even if MATLAB crashed or the acquisition was interrupted by a power cut.

Perform the following steps to resume an acquisition:

  • Select Sample > Resume Acquisition from the BakingTray menu. Load the recipe file from the acquisition directory containing the sample you wish to resume.

  • You will be asked to confirm whether you wish to resume the acquisition.

  • Press "Yes" and double-check the parameters in the recipe and prepare GUI.

  • You will then be presented with a new GUI asking how the acquisition should be resumed. e.g. if the last section was partially completed, should the existing data be discarded and the section re-imaged.

  • You are responsible for turning the PMTs back on. Similarly for ensuring the laser is on and the shutter is open.

  • The Acquisition GUI will now appear. Press "Bake" to start the acquisition. You only need to do another preview scan in exceptional circumstances (see below).

Do not re-load the recipe after you have asked to resume. This will revert important settings to default values.


  • It is not necessary to do another preview scan and repeat the auto-thresh under most circumstances. If you are re-starting the acquisition because of an issue related with the auto-ROI, or because somehow how the sample vanished, etc, then of course you should do another preview and another Auto-Thresh before pressing Bake.

  • If you have reason to think the sample surface might have moved (e.g. you have changed the blade) then you might want to take a preview scan first and repeat the auto-thresh. Then watch how it cuts and tweak objective height.

Last updated