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Task #5396 (accepted)

Opened 10 years ago

Last modified 5 years ago

Parse ROIs from .vsi files

Reported by: mlinkert Owned by: rleigh
Priority: major Milestone: ROI
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: smithd@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 1.0d
Sprint: n.a.

Description

See for example cellsens/melissa/SW...GOLD copy.vsi, which has 3 ROIs:

  • "ROI 1", a red rectangle with line width of 5 and upper left corner at approximately (901, 931)
  • "ROI 2", a green circle of radius ~510 with center at ~(7330, 5190)
  • "ROI 3", a yellow polygon (roughly trapezoidal) in the upper right corner. It also has a different font from the others.

Change History (19)

comment:1 Changed 10 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3.1 to OMERO-Beta4.3.2

comment:2 Changed 10 years ago by mlinkert

  • Remaining Time set to 1
  • Sprint set to 2011-07-21 (1)

We have now received sufficient documentation to solve this problem.

comment:3 Changed 10 years ago by cxallan

  • Sprint changed from 2011-07-21 (1) to 2011-08-04 (2)

Moved from sprint 2011-07-21 (1)

comment:4 Changed 9 years ago by cxallan

  • Sprint changed from 2011-08-04 (2) to 2011-08-18 (3)

Moved from sprint 2011-08-04 (2)

comment:5 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [12ca71392c2763d1a1535f03d6e98153b0c65757/bioformats.git]) Finally implemented basic VSI tag parsing.

This is by no means comprehensive, but it at least lets us read out the
dimension ordering so that pixel data is now correct. It's also the
foundation for more advanced metadata parsing, e.g. ROIs.

Closes #6280, see #5396.

comment:6 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [12ca71392c2763d1a1535f03d6e98153b0c65757/bioformats.git]) Finally implemented basic VSI tag parsing.

This is by no means comprehensive, but it at least lets us read out the
dimension ordering so that pixel data is now correct. It's also the
foundation for more advanced metadata parsing, e.g. ROIs.

Closes #6280, see #5396.

comment:7 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [7864934e953ad5acd1e9eb969370cdd333c81347/bioformats.git]) Finally implemented basic VSI tag parsing.

This is by no means comprehensive, but it at least lets us read out the
dimension ordering so that pixel data is now correct. It's also the
foundation for more advanced metadata parsing, e.g. ROIs.

Closes #6280, see #5396.
(cherry picked from commit 12ca71392c2763d1a1535f03d6e98153b0c65757)

comment:8 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [7864934e953ad5acd1e9eb969370cdd333c81347/bioformats.git]) Finally implemented basic VSI tag parsing.

This is by no means comprehensive, but it at least lets us read out the
dimension ordering so that pixel data is now correct. It's also the
foundation for more advanced metadata parsing, e.g. ROIs.

Closes #6280, see #5396.
(cherry picked from commit 12ca71392c2763d1a1535f03d6e98153b0c65757)

comment:9 Changed 9 years ago by mlinkert

  • Sprint changed from 2011-08-18 (3) to 2011-09-01 (4)

comment:10 Changed 9 years ago by mlinkert

  • Status changed from new to accepted

comment:11 Changed 9 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3.2 to Unscheduled
  • Sprint 2011-09-01 (4) deleted

comment:12 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to OMERO-Beta4.4

comment:13 Changed 9 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.4 to Unscheduled

Best to look at this as part of the upcoming ROI work, rather than trying to squeeze it in before 4.4.

comment:14 Changed 9 years ago by jburel

Referencing ticket #3215 has changed sprint.

comment:15 Changed 8 years ago by rleigh

  • Owner changed from mlinkert-x to rleigh

comment:16 Changed 8 years ago by jamoore

Referencing ticket #3215 has changed sprint.

comment:17 Changed 5 years ago by jamoore

  • Milestone changed from Unscheduled to ROI

comment:18 Changed 5 years ago by jamoore

Referencing ticket #3215 has changed sprint.

comment:19 Changed 5 years ago by jamoore

Referencing ticket #3215 has changed sprint.

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