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Add support for reading external ImageSeries

Open oruebel opened this issue 6 years ago • 0 comments

2) Feature Request

ImageSeries allows specification of data via external_file image stacks. It would be useful to enhance the ImageSeries Container class in PyNWB to support reading of ImageSeries from these external image stacks. Currently this is up to the user. Specifically we should

  • Improve documentation of external_file and starting_frame to clarify the use and meaning of the fields, supported external formats etc. Both in the API and schema
  • Add class ExternalImageStack that encapsulates an external image stack and allows reading from a stack of images
  • Update ImageSeries.data to support providing an ExternalImageStack as input to simplify creating an ImageSeries for an external image stack
  • Add helper function ExternalImageStack.from_dir to create the external_file and starting_frame fields for the ImageSeries and simplify using external image stacks with fixed filename conventions

Problem/Use Case

Image acquisition systems often store image stacks in standard TIFF image stacks. NWB supports this in ImageSeries by allowing include of the stacks directly, rather than copy of the data. This feature would users with interacting with those external image stacks.

CC: @nclack @ln-vidrio

Checklist

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oruebel avatar Sep 13 '19 23:09 oruebel