problems in importing aligned tilt series/process on different machines

[Qiuye Li]

Hi all,

I got the error message "Invalid URI: The URI is empty" when I tried to import aligned tilt series back to warp (actually it showed up before I specified the alignment files). Any ideas for this kind of situation?

One possible related context is that the data are processed and exported (as unaligned TS) on the facility K3 computer, and then moved to our lab computers for further processing. Would this be a problem? If so, is there any workarounds? I actually modified the SubFramePath in the *.mrc.mdoc file to match the new location, but still saw the same error.

Any help and suggestions will be greatly appreciated.

Qiuye

[Mathew McLaren]

Hi Quiye,

Warp (or maybe Windows in general) struggles with some types of network shares. If you mount it as a drive with a drive letter then I think it should be more successful. However, you should just be able to copy the .xf files from your tilt series reconstructions back over to your (Warp) imod folder, which should be enough to pass to the next step. As far as I'm aware, Warp can only use the .xf file from IMOD, Aretomo or similar for alignment information.

Cheers,

Mat

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[Qiuye Li]

Hi Mat,

Thanks for your reply. After some quick tests I got a better understanding of warp's logic, even though I haven't reached the bottom of it I think it's worth reporting back here. 

My original problem was actually 'recognizing' those linked files (i.e, the movie and mdoc). After some tests, I realized that my .mdoc files can be used as is, but preprocessing and tomogram generation must be done on the same computer. Furthermore, if I rename a project directory, it will fail even on the same computer. This does not interrupt my workflow much but there should be a way to resolve it, I believe?

Additionally, I also realized that the correct alignment file should be named like XXX.mrc.xf, to be properly recognized. 

Best,

Qiuye

[Matthias Vorländer]

Hi,

did you check if the decimal settings under windows are correct? Depending on your system, regional settings for number formats (comma or dot) can be different, causing issues when mdoc files are read in. 

Best, Matthias 

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