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Task #4085 (closed)

Opened 9 years ago

Closed 8 years ago

Update OME-TIFF web site to reflect proposed modifications

Reported by: crueden-x Owned by: crueden-x
Priority: critical Milestone: OMERO-Beta4.3.2
Component: Documentation Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by crueden-x)

I sent an email to the ome-devel mailing list with a list of proposed augmentations to the OME-TIFF format, arrived at through discussion with other OME developers and interested parties. In summary:

  1. Allow OME-TIFF datasets to use BigTIFF, rather than normal 32-bit TIFF, as appropriate.
  2. Update the recommended filename extension from .tif to .ome.tif, for clarity.
  3. Include an XML comment at the top of the OME-XML metadata block with a warning to those who would edit the block by hand.
  4. Store a hash (SHA1) of the pixel data associated with each TiffData? element.
  5. Store a hash (SHA1) of the OME-XML metadata in a custom TIFF tag.

The OME-TIFF web site needs to be updated to include these ideas, and our sample data should also reflect the recommendations as closely as possible (probably easiest to use an updated Bio-Formats to write new sample OME-TIFF files; see ticket #82).

Change History (9)

comment:1 Changed 9 years ago by jmoore

imported from bio-formats:#80

comment:2 Changed 9 years ago by crueden-x

  • Description modified (diff)
  • Owner changed from curtis to crueden-x
  • Reporter changed from curtis to crueden-x

comment:3 Changed 8 years ago by ajpatterson

Make sure all this was included in the pages on ome-xml.org when moving content over.

comment:4 Changed 8 years ago by ajpatterson

  • Milestone changed from Unscheduled to OMERO-Beta4.3.2

comment:5 Changed 8 years ago by ajpatterson

Referencing ticket #2296 has changed sprint.

comment:6 Changed 8 years ago by crueden-x

The OmeTiffSpec page has been updated. Items 1, 2 and 3 above are integrated. I also added a section on embedding OME-XML into only a subset of the TIFF files, which can greatly reduce file size when storing one plane per OME-TIFF, but also reduces redundancy. And I added more section summaries to make the prose easier to read.

Regarding item 4, I did not mention the ability to embed a SHA1 per image plane, since that is not OME-TIFF-specific. And I did not mention anything with respect to item 5 because as far as I know, we never added a standard way to store a SHA1 of the OME-XML metadata.

comment:7 Changed 8 years ago by jburel

Referencing ticket #2296 has changed sprint.

comment:8 Changed 8 years ago by crueden-x

The artificial sample data on the OmeTiffData page has been updated to the 2011-06 schema, using the MakeTestOmeTiff data generator, which has been overhauled and migrated to the loci.formats.tools package.

comment:9 Changed 8 years ago by crueden-x

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