Task #5114 (closed)
BUG: Tile ordering is not correct for all .vsi files
| Reported by: | mlinkert | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.3.2 |
| Component: | Bio-Formats | Version: | n.a. |
| Keywords: | n.a. | Cc: | smithd@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-07-21 (1) |
Description
Single-channel and 24-bit RGB files seem fine, but anything with multiple planes and/or multiple .ets files has subtle errors in the tile ordering.
It's not entirely clear how to detect or correct for this, as (near as I can tell) there is no tile index.
Change History (10)
comment:1 Changed 8 years ago by Melissa Linkert <melissa@…>
comment:2 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [336062fc2289c5c84803c4acd4a91e0cf387e4e4/bioformats.git]) Lots of work on dimension detection and tile reading.
The cellSens reader now mostly works; closes #4156.
There are still a few wrinkles left to iron out though - see #5114.
comment:3 Changed 8 years ago by mlinkert
- Cc smithd@… added
comment:4 Changed 8 years ago by mlinkert
- Sprint changed from 2011-05-19 (12) to 2011-06-02 (13)
comment:5 Changed 8 years ago by mlinkert
- Status changed from new to accepted
comment:6 Changed 8 years ago by mlinkert
- Milestone changed from OMERO-Beta4.3 to OMERO-Beta4.3.1
- Sprint 2011-06-02 (13) deleted
[e35079dc5e8457f5a2e762a9b4fca5c27128fde7/bioformats.git] fixes a few more problems here, so that in the case of multiple .ets files at least the first one will be read correctly. Datasets with multiple planes are still not correctly supported, though.
As mentioned previously, the solution to this problem is not obvious. So for 4.3, the plan is to release .vsi support with multi-plane datasets specifically not supported. We've been promised .vsi specifications from Olympus, so as soon as those arrive we will add proper support for multiple planes.
comment:7 Changed 8 years ago by mlinkert
- Milestone changed from OMERO-Beta4.3.1 to OMERO-Beta4.3.2
comment:8 Changed 8 years ago by mlinkert
- Remaining Time set to 1
- Sprint set to 2011-07-21 (1)
We have now received sufficient documentation to fix this problem.
comment:9 Changed 8 years ago by Melissa Linkert <melissa@…>
- Remaining Time changed from 1 to 0
- Resolution set to fixed
- Status changed from accepted to closed
(In [3861b4944c57a2ce1707b7920b84072ec6641be2/bioformats.git]) Fix tile dimensions.
Closes #5114.
comment:10 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [3861b4944c57a2ce1707b7920b84072ec6641be2/bioformats.git]) Fix tile dimensions.
Closes #5114.
(In [336062fc2289c5c84803c4acd4a91e0cf387e4e4/bioformats.git]) Lots of work on dimension detection and tile reading.
The cellSens reader now mostly works; closes #4156.
There are still a few wrinkles left to iron out though - see #5114.