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- Timestamp:
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03/04/10 16:17:35 (14 years ago)
- Author:
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wmoore
- Comment:
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initial
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v1
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| 1 | | Add EMAN functionality to OMERO using Python scripts. |
| | 1 | Investigate the options for using OMERO as the image repository for single particle analysis work-flows. This is a very ambitious task to do properly, and will probably require significant help from developers of the single-particle software. Current aim is to see whether a proof of principle is possible. |
| 2 | 2 | |
| 3 | | These can be client scripts, or server-side scripts (scripting service). |
| | 3 | Example workflows: |
| | 4 | * http://www.wadsworth.org/spider_doc/spider/docs/techs/recon/mr.html |
| | 5 | * http://people.chem.byu.edu/belnap/pft3dr/tutorial/tutorial.html |
| | 6 | * http://blake.bcm.edu/emanwiki/EMAN2/Tutorials |
| | 7 | |
| | 8 | Importantly, EMAN2 is written in Python, and SPIDER has some Python scripts (full bindings in development). |
| | 9 | |
| | 10 | The 2 main options are (as always): |
| | 11 | |
| | 12 | == Client-side software == |
| | 13 | E.g. Have SPIDER or EMAN2 running on the client. Adapt existing scripts to access data on OMERO. Shouldn't be too hard to do with individual scripts using small numbers of images. But when many large images are required, this becomes impracticable. |
| | 14 | |
| | 15 | == Server-side software == |
| | 16 | Use the OMERO scripting service to call Python functions in SPIDER or EMAN installed on the server. Scripts will still have to convert pixel data into the correct file type (temporary data duplication), but won't have to move data over the wire. |
| | 17 | |
| | 18 | == EMAN2 == |
| | 19 | Currently EMAN2 is looking like a good option for Python-based processing. Investigating early steps of Single-particle analysis, with server-side scripts called via the scripting service: |
| | 20 | |
| | 21 | These include: |
| | 22 | 1. Particle picking [http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/EMAN2/boxer.py boxer.py] |
| | 23 | 1. Generating particle images from ROIs [http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/EMAN2/imagesFromRois.py imagesFromRois.py] |
| | 24 | 1. CTF estimation and filtering |
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