Ticket #398 (closed enhancement: fixed)

Opened 11 years ago

Last modified 9 years ago

Better support for N-dimensional data

Reported by: curtis Owned by: curtis
Priority: major Milestone: bio-formats-5.0
Component: bio-formats Severity: serious
Keywords: Cc:
Blocked By: Blocking:

Description

Eliminate IFormatReader.getChannelDimTypes and IFormatReader.getChannelDimLengths, in favor of more comprehensive getDimTypes and getDimLengths methods, which return all used dimensions in correct rasterization order.

  • OME dimensions include: X, Y, Z, C, T
  • Examples of non-OME dimensions:
    • lifetime bins
    • excitation wavelength
    • polarization
    • screen
    • plate
    • well
    • field

Advantages:

  • fully capable of expressing N-dimensional image data
  • allows for XZ scans and other spatial configurations
  • eliminates the need for DimensionOrder and Interleaved core metadata

Work to do:

  1. Rework ChannelSeparator a little
    • It should always "pull" XY to the front
  1. Rework DimensionSwapper; it is more complex now
  1. Rework DataBrowser to use new methods, displaying extra sliders as before
  1. Rework FileStitcher and AxisGuesser a bit
    • Guessed axes become new dimensions
  1. Change anywhere else that calls getChannelDim* methods
  1. InCell reader can be retrofitted to use this new functionality
    • Certain other readers can benefit as well: Flex, Fluoview, ...
  1. Initially, conversion to OME-TIFF with bfconvert should throw an exception if any dimensions beyond 5D exist, since there is nowhere in the OME-XML schema to store the extra dimensional information

Change History

comment:1 Changed 10 years ago by melissa

  • Milestone changed from bio-formats-4.2 to bio-formats-5.0

comment:2 Changed 9 years ago by curtis

  • Status changed from new to closed
  • Resolution set to fixed

moved to  ome:#4114

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