Filament particle extraction from EMAN2-segmented filaments

[shujun cai]

Dear Mailing List,

I was wondering if it is possible to extract particles from filaments segmented by EMAN2.

Best,

Shujun

[Steve Ludtke]

Yes, but which program did you use to extract the filaments. I think there are 3 different ways to do it...  I assume you're trying to do IHRSR style averaging or somesuch?

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[shujun cai]

Yes. The programs I have used previously are RELION 5 and PEET. If the filaments are segmented automatically in EMAN2, would it be possible to use EMAN2 to extract particles from those segmentations?

Best,

Shujun

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[Steve Ludtke]

Hi Shujun,

if you want suggestions of what to do, we're going to need to know exactly what you have now, and what you're hoping to get. Your statement is too vague to provide any advice. Filaments can be identified and extracted in a variety of ways depending on your goals and the type of filament. 

Right now, you presumably have micrographs (averaged movies), and it sounds like you have some sort of existing annotations of where the filaments are?  Is that true? Or are you talking about tomography, in which case you might have tomograms instead. In what format are your current annotation files?  Annotation files come in many varieties. In some cases they may just be the coordinates of the start of a filament and the coordinates of the end of the filament. Other strategies have a list of coordinates following the path of the filament (important if the filaments are not very straight, but done with different tools). Or maybe you already have extracted filaments as a set of rectangular images where the filaments have already been aligned so they are centered in the cylindrical region?  Maybe you don't have annotations at all yet, and you're looking for suggestions of which tools to use to find the filaments in the first place?

Anyway, if you can clearly explain your situation, people on the list can comment about strategies for doing what you're trying to do. If you have annotation files, you might consider including an example annotation file with your next post so we can see what format its in (they are usually quite small). 

cheers

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[shujun cai]

Hi Steve,

I have tomograms containing filaments that were segmented in EMAN2, so I have .hdf files with the segmentation information. EMAN2 has a "Find particles from segmentation" function for particle extraction, but I'm not sure whether it can also be used for filamentous structures. If not, is there another way to extract particle coordinates from the EMAN2 .hdf segmentation file?

Best,

Shujun

[Steve Ludtke]

Ok, thanks, that helps give some context. 

So you have .hdf files containing extracted segments from tomograms which you also have, and you are hoping to extract the geometry information from the .hdf headers of the segments to locate where they were extracted from?  Am I getting that right?  You don't have access to the original EMAN2 project folder?  The info/ folder in the project is the primary place where all of the metadata used for the extraction itself is stored. If you only have the .hdf files and the tomograms, it may still be possible, but it would depend on which specific tool was used to do the extraction. You can see all of the metadata stored in the .hdf file header with 

e2iminfo.py -H file.hdf

That will just show the metadata for the first image in the file, but will give you an idea of what's present. If the necessary metadata is present, I can give you some tips on how to best extract the information. Ostensibly all of the standard header metadata items available are documented here: https://blake.bcm.edu/emanwiki/doku.php?id=eman2:metadata  but sometimes someone writes a program and neglects to update that page, so you may find items which aren't documented there. If so, just ask and we can help you figure it out.

If you don't see anything related to the original tomogram geometry in the HDF header, you'd need the original EMAN2 project folder to find that information.

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