Leginon

upload the metadata of the reconstructed 3D tomogram, full or subvolume, to Appion database. This requires that the tilt series is acquired through Leginon to make the association. Once uploaded, the tomogram is transformed to Leginon/Appion coordinate system, and a z-projection (full tomogram) or slicing movie (sub tomogram) is created as if it is created through Appion pipeline. Therefore, further processing is possible.

Anchi

Thanks Anchi. Some more questions:

1. By "upload the metadata of the reconstructed 3D tomogram to Appion database", do you mean a 3D tomogram reconstructed through Appion or by other method outside of Appion?

2. After I use "Align Tilt Series / Create full tomogram" under Tomography on Appion Data Processing, in our case - RAPTOR, is the resulting tomogram already in the Appion database, or do I need to go through "upload tomogram"?

3. How do I view Appion database (list of tomograms, tilt series, etc.)?

1. I meant a 3D tomogram made outside appion pipeline.

2. Raptor alignment is recorded in Appion database. If you continue and use the "create full tomogram" tool to make the 3d tomogram, it is in the appion database, too. Therefore, you don't need to upload.

3. Like alignment results, once full tomogram is made, you should find them in the same appion processing webpage either next to "tomography" menu list in the format of 12/0 where
the first number refers to how many full tomograms are in the appion database for this Leginon session. The second number refers to how many subvolume is extracted from the full tomograms. You can click on the number to bring up the summary page for tomograms and find the query used through that and other pages it has links to.

Thanks Anchi.
After RAPTOR generates a 3D tomogram, we would like to generate a movie (going through slices, smaller dimension) and a central slice image too. I think you already have these functions build in? If yes, could you please point to me some example code to demonstrate how to call them?

Another question: After RAPTOR generates the 3D tomogram, what is the web download link to the tomogram file? I did not find download links at the current Tomography summery page.

1. The functions are apTomo.makeMovie and apTomo.makeProjection. Like most appion function called by python scripts, apTomo.py is in myami/appion/appionlib in your svn check out and in your python site-packages directory once installed. You should be able to find call example in myami/appion/bin/subtomomaker.py

2. We didn't put a link for download. It is a reasonable idea, although I wonder how long it will take over the network. You can add it following examples in myamiweb/processing. Just search for the word download in any php file. BTW, I did not make center slice, just projections, in these.