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Per-micrograph image shift for beam tilt refinement

Added by Michael Cianfrocco over 5 years ago

Hi Anchi,

Do you have a mysql command to get image shift per micrograph? I see the image shift is stored in the database and there is the example command for the image shift output summary:

SELECT UNIX_TIMESTAMP(`a`.`DEF_timestamp`) AS `unix_timestamp`, `a`.`DEF_timestamp` AS `timestamp`, `p`.`name`, `s`.`SUBD|image shift|x` AS `image_shift_x`, `s`.`SUBD|image shift|y` AS `image_shift_y` FROM `AcquisitionImageData` AS `a` LEFT JOIN `PresetData` AS `p` ON (`p`.`DEF_id`=`a`.`REF|PresetData|preset`) LEFT JOIN `ScopeEMData` AS `s` ON (`s`.`DEF_id`=`a`.`REF|ScopeEMData|scope`) WHERE `a`.`REF|SessionData|session`=896 AND `p`.name='en'

But I'm not familiar with mysql to figure out how to get per micrograph beam shift.

This is to try to use for RELION beam tilt refinement, grouping data into beam tilt groups.

Thanks!
Mike


Replies (3)

RE: Per-micrograph image shift for beam tilt refinement - Added by Anchi Cheng over 5 years ago

On FEI scopes beam shift is changed internally according to user image shift. Leginon therefore does not get to see what beam shift is changed to compensate the image shift applied.

Given that any image shift needs this compensation linearly applied, you can give Relion the image shift values instead and grouping that as your beam tilt groups.

If you have by now calibrated beam-image shift aberration, there is also the possibility of using this feature: Issue #5884

RE: Per-micrograph image shift for beam tilt refinement - Added by Michael Cianfrocco over 5 years ago

Thanks Anchi! What is the best way to get the image shift values per micrograph from the database?

RE: Per-micrograph image shift for beam tilt refinement - Added by Michael Cianfrocco over 5 years ago

Never mind, we were able to figure it out on our end:

SELECT UNIX_TIMESTAMP(`a`.`DEF_timestamp`) AS `unix_timestamp`, `a`.`DEF_timestamp` AS `timestamp`, `a`.`filename`, `p`.`name`, `s`.`SUBD|image shift|x` AS `image_shift_x`, `s`.`SUBD|image shift|y` AS `image_shift_y` FROM `AcquisitionImageData` AS `a` LEFT JOIN `PresetData` AS `p` ON (`p`.`DEF_id`=`a`.`REF|PresetData|preset`) LEFT JOIN `ScopeEMData` AS `s` ON (`s`.`DEF_id`=`a`.`REF|ScopeEMData|scope`) WHERE `a`.`REF|SessionData|session`=896 AND `p`.name='en';

Thanks,
Mike

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