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Bug #7076

closed

Unstable beam position when preset change involves spot size change on Talos column

Added by Anchi Cheng over 5 years ago. Updated about 4 years ago.

Status:
Closed
Priority:
High
Assignee:
Anchi Cheng
Category:
-
Target version:
Appion/Leginon 3.5
Start date:
03/24/2019
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.3
Show in known bugs:
No
Workaround:

Description

The root cause of it are three folds:

1. TUI lens normalization is used on Talos column instead of preset cycling.

1. TUI normalization settings allows only and default to normalize spotsize and intensity. However, spot size change moves beam position and camera. It requires normalization of minicondenser to be consistent with the position aligned through the alignment procedure of spot-dependent gun shift.

2. Leginon send spot size after magnification change, but we only added additional normalization in magnification step.

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 #1

Updated by Anchi Cheng over 5 years ago

  • Subject changed from TFS Talos series beam is not stable when preset change involves spot size change to Unstable beam position when preset change involves spot size change on Talos column
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 #2

Updated by Anchi Cheng over 5 years ago

Had to change back the default set order to magnification first and then spot size since microscope has internal memory of spot size per projection submode. Change spotsize before changing magnification confuses it and resulted in inconsistent timing. Created a work-around specific for Talos column.

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 #3

Updated by Anchi Cheng over 5 years ago

Moved normalization after intensity change since that is needed, too. This removes spotsize/mag order conflict. Therefore, instrument.py change can be reverted.

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 #4

Updated by Anchi Cheng about 4 years ago

  • Status changed from Assigned to Closed
  • Target version changed from Appion/Leginon 3.4 to Appion/Leginon 3.5

This now works.

Usage:

If you have a scope with Talos column, set fei.cfg

FORCE_NORMALIZE_ALL_AFTER_SETTING = True

Note: This does slow down the data collection. Alternatively, you can turn off all normalizations on the TUI and use cycling presets in PresetsManager. In other words, use it as if it is a Tecnai scope that does not do lens normalization. However, this will make your manual alignment using TUI behaves different from within Leginon, not very good for high res data collection.

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