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Ticket #315 (closed enhancement: fixed)

Opened 2008-08-01T02:23:33-05:00

Last modified 2009-04-23T10:17:13-05:00

Investigate how to handle ROIs and overlays within proprietary file formats

Reported by: melissa Owned by: melissa
Priority: major Milestone: bio-formats-4.1
Component: bio-formats Severity: non-issue
Keywords: Cc: h.sluiman@…, terjung@…
Blocked By: Blocking:


Several supported file formats can contain overlays - notably Zeiss ZVI, Zeiss LSM and Nikon ND2. It would be nice if there were some way to convert the overlay data into a common format, in such a way that the ImageJ plugin could retrieve and optionally display overlays.

Change History

comment:1 Changed 2008-08-01T13:43:16-05:00 by curtis

The Bio-Rad PIC specification also supports overlays.

I suggest we use OME-XML for overlays, once the next major revision of the specification is released, since it will contain constructs for representing overlay-style ROIs.

Once the readers properly parse the overlays, we will still need to implement support for rendering them in ImageJ, the Bio-Formats Image Viewer, and/or other supported viewers.

comment:2 Changed 2009-02-20T10:19:19-06:00 by melissa

  • Cc terjung@… added
  • Summary changed from Investigate how to handle overlays within proprietary file formats to Investigate how to handle ROIs and overlays within proprietary file formats
  • Milestone set to bio-formats-4.1.0

FV1000 OIB/OIF files can also contain ROIs/overlays.

comment:3 Changed 2009-04-01T13:59:10-05:00 by melissa

(In [4965]) Most ROI types are now parsed from FV1000 files. See #315.

comment:4 Changed 2009-04-01T14:40:26-05:00 by melissa

(In [4966]) The ImageJ plugin can now (optionally) display the ROIs stored in a file. See #315.

comment:5 Changed 2009-04-13T14:17:20-05:00 by melissa

(In [4997]) Added preliminary support for ROIs to ZeissLSMReader; some ROI types are still unsupported. See #315.

comment:6 Changed 2009-04-21T15:33:11-05:00 by melissa

(In [5018]) Reduced ZVI initialization time and updated the ZVI reader to parse data for ellipse and rectangle ROIs. See #315 and #377.

comment:7 Changed 2009-04-22T14:27:21-05:00 by melissa

(In [5019]) Updated ZVI reader to support additional ROI types. See #315.

comment:8 Changed 2009-04-23T10:17:13-05:00 by melissa

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

(In [5020]) Added ROI support to NativeND2Reader. Closes #315.