Task #5937 (closed)
Add simple stitching option to ImageJ plugin
| Reported by: | mlinkert | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.3.1 |
| Component: | Bio-Formats | Version: | n.a. |
| Keywords: | n.a. | Cc: | |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-07-07 (1) |
Description
With the 4.3.0 release, we changed how tiles in ZVI files are handled; instead of doing simple stitching (i.e. no accounting for overlap) internally, each tile is now treated as a separate series.
However, in some cases it would be nice to have the simply stitched image. The best solution is probably in two parts:
- make a ReaderWrapper? implementation that does the actual "stitching" based on stage coordinates
- add a checkbox to the ImageJ import plugin that, when checked, will add the new ReaderWrapper? implementation to the reader stack
Change History (11)
comment:1 Changed 13 years ago by mlinkert
- Sprint set to 2011-07-07 (1)
comment:2 Changed 13 years ago by Melissa Linkert <melissa@…>
comment:3 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [c9a5b97e7f95378f03710154e3723d0af0291c40/bioformats.git]) Add checkbox that turns on tile stitching.
See #5937.
comment:4 Changed 13 years ago by Melissa Linkert <melissa@…>
- Remaining Time changed from 1 to 0
- Resolution set to fixed
- Status changed from new to closed
(In [9790576be7088c7d6fb0f0f60b0f985b8c30a138/bioformats.git]) Lay out tiles based upon the actual coordinates.
This is more reliable than trying to sort the coordinates, especially if
there are some tiles that do not have coordinates (as is not uncommon in
ZVI files).
Also, add some checks to make sure that we do not try to stitch together
series with different dimensions.
Closes #5937.
comment:5 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [4c307635dc22b1d1c5e50af1ba0060171ca848b9/bioformats.git]) Initial version of TileStitcher?.
This is a new ReaderWrapper? implementation that performs simple
stitching on the underlying tiles. It assumes 0% overlap, and relies
upon the stage coordinates to position the tiles correctly.
See #5937.
comment:6 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [c9a5b97e7f95378f03710154e3723d0af0291c40/bioformats.git]) Add checkbox that turns on tile stitching.
See #5937.
comment:7 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [9790576be7088c7d6fb0f0f60b0f985b8c30a138/bioformats.git]) Lay out tiles based upon the actual coordinates.
This is more reliable than trying to sort the coordinates, especially if
there are some tiles that do not have coordinates (as is not uncommon in
ZVI files).
Also, add some checks to make sure that we do not try to stitch together
series with different dimensions.
Closes #5937.
comment:8 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [4c307635dc22b1d1c5e50af1ba0060171ca848b9/bioformats.git]) Initial version of TileStitcher?.
This is a new ReaderWrapper? implementation that performs simple
stitching on the underlying tiles. It assumes 0% overlap, and relies
upon the stage coordinates to position the tiles correctly.
See #5937.
comment:9 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [c9a5b97e7f95378f03710154e3723d0af0291c40/bioformats.git]) Add checkbox that turns on tile stitching.
See #5937.
comment:10 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [4c307635dc22b1d1c5e50af1ba0060171ca848b9/bioformats.git]) Initial version of TileStitcher?.
This is a new ReaderWrapper? implementation that performs simple
stitching on the underlying tiles. It assumes 0% overlap, and relies
upon the stage coordinates to position the tiles correctly.
See #5937.
comment:11 Changed 13 years ago by Melissa Linkert <melissa@…>
(In [c9a5b97e7f95378f03710154e3723d0af0291c40/bioformats.git]) Add checkbox that turns on tile stitching.
See #5937.
(In [4c307635dc22b1d1c5e50af1ba0060171ca848b9/bioformats.git]) Initial version of TileStitcher?.
This is a new ReaderWrapper? implementation that performs simple
stitching on the underlying tiles. It assumes 0% overlap, and relies
upon the stage coordinates to position the tiles correctly.
See #5937.