Task #3918 (closed)
Import of Spider and IMAGIC formats
| Reported by: | wmoore | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.3 |
| Component: | Import | Version: | n.a. |
| Keywords: | n.a. | Cc: | |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-04-21 (10) |
Description (last modified by wmoore)
These two files are of specific interest to EM users.
See
- http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html
- http://www.imagescience.de/formats/formats.htm
Need to get some sample data. Spider data from a Nature Protocols publication is available from their web-site.
http://www.wadsworth.org/spider_doc/spider/docs/protocol_download.html
Attachments (6)
Change History (18)
comment:1 Changed 9 years ago by wmoore
- Description modified (diff)
- Milestone changed from Unscheduled to OMERO-Beta4.3
comment:2 Changed 8 years ago by Melissa Linkert <melissa@…>
comment:3 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [58d54dda93ef2e85b5f2f338df50765288b4f3a1/bioformats.git]) Add support for SPIDER EM files. See #3918.
comment:4 Changed 8 years ago by mlinkert
- Remaining Time set to 0.5
- Sprint set to 2011-04-21 (10)
It looks like we can generate IMAGIC sample data using em2em: http://www.imagescience.de/em2em/index.htm
comment:5 follow-up: ↓ 8 Changed 8 years ago by wmoore
Hi Melissa - thanks for this.
I just tested Spider support with the 3 sample files Ardan sent me (I'll attach them)
- The singleImage.spi opened OK
- The volume.spi opened OK but looks like the wrong data type is used (alternative planes are inverted contrast)
- The imageStack.stk appears not to be supported, although if I rename it to .spi it opens OK but appears as a single plane image. Opening in EMAN2 (after renaming to .spi) shows it is 4 separate planes (64x64) from different images. I think we should probably import this as 4 Z-planes, since this is what users are used to. I'll attach the files and screen-shots from EMAN.
Probably the '.stk' is just a convention to indicate that the file is a stack, rather than a completely different format. EMAN2 seems to think so anyway.
NB: These files were written by XMIPP package, maybe not guaranteed to be 100% correct!
Changed 8 years ago by wmoore
Changed 8 years ago by wmoore
Changed 8 years ago by wmoore
Changed 8 years ago by wmoore
Changed 8 years ago by wmoore
Changed 8 years ago by wmoore
comment:6 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [8d1d6ad3955545d552f483ed843603a2ea8fd811/bioformats.git]) Add support for SPIDER EM files. See #3918.
comment:7 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [8d1d6ad3955545d552f483ed843603a2ea8fd811/bioformats.git]) Add support for SPIDER EM files. See #3918.
comment:8 in reply to: ↑ 5 Changed 8 years ago by mlinkert
Replying to wmoore:
Hi Melissa - thanks for this.
I just tested Spider support with the 3 sample files Ardan sent me (I'll attach them)
- The singleImage.spi opened OK
- The volume.spi opened OK but looks like the wrong data type is used (alternative planes are inverted contrast)
It does look a bit strange when opened using 'showinf', but seems fine to me in ImageJ/Fiji. Did you see this problem in ImageJ? If not, then it is probably just a contrast issue in showinf.
comment:9 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [7aecee363910afe7d0144e5742ce95a16c072b7d/bioformats.git]) Initial version of IMAGIC reader. See #3918.
comment:10 Changed 8 years ago by Melissa Linkert <melissa@…>
- Remaining Time changed from 0.5 to 0
- Resolution set to fixed
- Status changed from new to closed
(In [e77fb9d3c9ce3908aca3ef77dd6b4a8c3897887d/bioformats.git]) Update Spider reader to handle other types of stack data.
Stacks with one header per slice are now supported, as are files without
the "spi" extension. Closes #3918.
comment:11 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [7aecee363910afe7d0144e5742ce95a16c072b7d/bioformats.git]) Initial version of IMAGIC reader. See #3918.
comment:12 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [e77fb9d3c9ce3908aca3ef77dd6b4a8c3897887d/bioformats.git]) Update Spider reader to handle other types of stack data.
Stacks with one header per slice are now supported, as are files without
the "spi" extension. Closes #3918.
(In [58d54dda93ef2e85b5f2f338df50765288b4f3a1/bioformats.git]) Add support for SPIDER EM files. See #3918.