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Task #12730 (new)

Opened 5 years ago

Last modified 4 years ago

Add support for Tissuegnostics data

Reported by: omero-qa Owned by:
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: 5.0.8
Keywords: new-format, external Cc: dshumake@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by mlinkert)

https://www.openmicroscopy.org/qa2/qa2/qa/feedback/10470/

Comment: Tissue gnostics data file and viewer. In order for Omero to read these files.

See QA 10470 and https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7728. This is a digital pathology format, with each image tile stored in a separate file.

Change History (2)

comment:1 Changed 5 years ago by mlinkert

  • Component changed from from QA to Bio-Formats
  • Description modified (diff)
  • Keywords new-format external added
  • Priority changed from minor to major

comment:2 Changed 4 years ago by mlinkert

  • Owner mlinkert deleted

The QA issue contains one zip of an acquisition with 2 slides, and one zip of software that can read the slides on Windows.

The .aqproj file should be the only target for setId; this appears to contain the majority of the metadata, and can likely be parsed with loci.formats.services.POIService. The files in the "dat" folder can also be parsed with POIService, though it's not clear if/how useful they are. The 'olebrowse' command of https://bitbucket.org/decalage/oletools will be more useful than a standard hex editor here, since the .dat/.aqproj files are in a filesystem-like format.

As far as I can tell, the "Images" folder is just the highest resolution image and the "Cache" folder is the lower resolutions in the pyramid. Removing the "Cache" folder on Windows does impact the behavior of the TissueFaxs? viewer. Be aware that the JPEG tiles are 1600x1200, which is on the large side - it will be important to test importing and viewing in OMERO (especially web) to ensure that openBytes time and memory performance are acceptable.

As with most digital pathology formats, this is likely to be a little tricky to get exactly right, so I wouldn't suggest it as a first reader. I would also suggest studying SVSReader and CellSensReader? (if you're not already familiar with them), as a lot of the pyramid and tile manipulation can likely be modeled on those readers.

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