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Is it possible to perform image alignment before deconvolution using Autoquant connect?

I am batch processing files and sending them to Autoquant using Autoquant Connect. I would like to specify that Autoquant first performs an alignment of the stacks before performing the deconvolution. Is this possible using the Autoquant Connect file? (I do not manually want to perform an alignment).

Thanks in advance for any advice.

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    Answer ✓
    AutoQuant Connect is unfortunately limited to deconvolution commands at the present time. A couple of possible workarounds:

    First, though Connect itself doesn't cover alignment, the batch processing interface in AutoQuant does. So you could load up your datasets via Connect, then drag-and-drop them to the batch, and select Image Alignment for all of the tasks.

    That does involve some UI interaction, though, so if you prefer to script that away as well, another possibility might be with Image-Pro Premier or the older Image-Pro Plus, if you have either of those packages. Both include a scriptable alignment feature that you might be able to use to create your aligned stacks, and then send THOSE over to AutoQuant for deconvolution.

    Best Regards,


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    Thanks Andy, I do not have either of those packages, but since automation is essential to me I will look into it. 

    Thanks again.
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