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Batch Process in Autoquant

Is it possible to point Autoquant batch processing at a folder instead of having to load the images into the program first? This becomes cumbersome when lots of images stacks are involved.

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    Answer ✓

    To help ensure that necessary parameters have been set, AutoQuant does require that datasets be loaded into the software in order to be processed. However, there are a few ways to help expedite the process when working with hundreds or even thousands of stacks.

    Assuming that your data is stored such that each file represents a stack or otherwise complete dataset (as opposed to having each file represent one frame of a dataset, for example), then my first suggestion is to open a Windows Explorer to the folder containing your stacks, then drag them all directly to the batch window at once, as shown here:

    From AutoQuant X 3.0.4 onward, the collection of files will be loaded into the batch in the background, allowing you to set up the batch using the first entry while the remaining entries load.

    Start by selecting the task (e.g., 3D Deconvolution). If the “Valid?” column switches to “Yes” after that, then the task could launch as-is. If it continues to display, “No”, then click on the word “No” to open the deconvolution dialog to see what was flagged as invalid.

    Once the sets have completed loading, and once the first task has been set up, then you can copy whatever settings you need and launch the batched tasks in just a few clicks. Start by right-clicking on the row that’s been set up.

    You’ll notice the menu has some copy/paste options that are divided into a couple of categories: optics settings and operational settings. The “all settings” entries cover both categories.

    • Optics settings are those that are changed in the Data Manager pane on the left. If you had to update anything in that pane, you’ll probably want to include this category.
    • Operational settings are those that are changed in the task dialog (which usually means the 3D Deconvolution dialog). Because it also copies the task assignment itself, I recommend always including this category unless there’s a setting that emphatically needs to change across your sets.

    Next, you’ll want to paste your settings to the remaining rows. I recommend including the row you’re copying from in your selection. It doesn’t hurt anything, and it makes it easier to launch everything in fewer clicks.

    Also, as a tip, when you select rows in the batch window – whether it be just one, or multiple rows – click in the Row Header area of the appropriate row(s), as indicated below. By interacting with that area instead of the Row Data area, it is possible to use selection shortcuts like Click+Drag, Ctrl+Click, and Shift+Click. The latter – selecting the first row, scrolling to the bottom, then Shift-clicking the last row – is my preference for working with large numbers of sets. 

    When all of the rows are selected, right-click in the Row Data area of any row in the selected region, and choose a paste option. You can skip some waiting and some clicking interaction by choosing one of the “compound” options at the bottom, like “Paste Operational Settings and Launch” if you didn’t have to change any optics settings, or “Paste All Settings and Launch” if you did.

    I hope that helps streamline your workflow!


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    Awesome! This is very helpful.

    Unfortunately the images are stored as individual frames so I'll still have to take an extra step to build the stacks before getting into autoquant, but this will greatly streamline the downstream processing. 
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