Task #12205 (closed)
ND2 Stage Positions
| Reported by: | jamoore | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | 5.0.3 |
| Component: | Bio-Formats | Version: | 5.0.1 |
| Keywords: | n.a. | Cc: | aaron.ponti@…, Erik.Welf@…, sbesson |
| Resources: | n.a. | Referenced By: | https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
I have tried version 5.0.1 on a new ND2 file that has one additional dimension: stage positions (referred to as "X-Y" in the Nikon NIS software).
The file contains 4 stage positions each of which has 4 time points, 3 planes and 3 channels. In total, the file contains X/Y = 4 * T = 4 * Z = 3 * C = 3 = 144 images.
Bio-formats sees 5 series in the image, each of which has T = 4, Z = 3 and C = 3, for a grand total of 180 images.
The "virtual" 5th series recycles the images from the first one, although the indices are slightly out of phase. Please notice that if you want to use the NIS Viewer to check the file, it does not work correctly on the Mac.
See:
Change History (5)
comment:1 Changed 10 years ago by sbesson
- Cc Erik.Welf@… sbesson added
comment:2 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.3
comment:3 Changed 10 years ago by jamoore
- Referenced By set to https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats
comment:4 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
comment:5 Changed 10 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [3e522f2678de230bee3fb45ed7dfcd26eee940e1/bioformats.git] on branch develop) ND2: rework text annotation parsing so that dimensions are not overlooked
Fixes #12205.
PR opened for inclusion in 5.0.3: https://github.com/openmicroscopy/bioformats/pull/1182