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[tmodes <1643283@xxxxxxxxxxxxxxxxxx>]

This is already possible from the command line. Run "nona -m TIFF_multilayer -o prefix project.pto".
>From the GUI this can be achieved by a user defined output sequence. This will be included in the next release. 
For the current version you can already use the executor file from http://hg.code.sf.net/p/hugin/hugin/file/3cfe92e88f17/src/hugin1/executor/normal_layered_tiff.executor

** Changed in: hugin
       Status: New => Fix Committed

** Changed in: hugin
    Milestone: None => 2016.4beta1

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https://bugs.launchpad.net/bugs/1643283

Title:
  Export with layers aligned

Status in Hugin:
  Fix Committed

Bug description:
  It would be great to be able to export panoramas with layers aligned.
  In some cases panorama images might require manual stitching. This is especially important when images are of different focus, shot with idea to do focus-stacking later.
  PTGui allows to export to PDF with layers aligned.
  While PDF is not a requirement, TIFF should suffice because layers are also supported by TIFF

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