Error importing AFIS / Beamtilt Groups

[martin]

Hi,
I’m having a few problems running the Import Movies job while trying to include the .xml files for beam-tilt grouping as per the guide. As far as I can see, CryoSPARC locates the xml files properly, but then issues an Exception: list index out of range error. For example, from the log:

Example movie/mic name for XML correspondence, after applying prefix/suffix cut:
FoilHole_17961633_Data_17929925_5_20250418_160501_Fractions
Example XML name for movie/mic correspondence, after applying prefix/suffix cut:
FoilHole_17961633_Data_17929925_5_20250418_160501_Fractions
Error parsing XML file /XXXXXXX/XXXXXX/raw/XXXXXX/Images-Disc1/GridSquare_17913661/Data/FoilHole_17961633_Data_17929925_5_20250418_160501_Fractions.xml
Exception: list index out of range

Am I missing something obvious? This is using the current version of EPU (3.11) and CryoSPARC 4.6.2

Advice appreciated!

[kookjookeem]

Hello,

Although I think EPU would provide properly formatted XML files, I would check if the XML files follow the format shown here.

XML file format for image shift groups

Dear @wrice, Just chiming in to show an example of the XML file format that CryoSPARC Import Movies/Micrographs and Import Beam Shift now expects. The only field from the XML file that is read by CryoSPARC is the BeamShift (the _x and _y attributes). This field is arranged as follows within the tree: <MicroscopeImage xmlns="http://schemas.datacontract.org/2004/07/Fei.SharedObjects" xmlns:i="http://www.w3.org/2001/XMLSchema-instance"> <microscopeData> <optics> <BeamShift…

Best,
Kookjoo

[martin]

Hmm, no, there is no beamtile data in the generated xml files. As far as I understand, EPU has now been modified to write out an AFIS group in the file name as described here:

Creating Optics Groups from EPU AFIS data and more

This also describes a workaround by grouping the exposures post-import, but I wonder if it might be possible to allow CryoSPARC to do this automatically without the xml files.