Leginon

h1. New User Features 33

h2. FEI Volta Phase Plate Integration

Automated control of holeless Volta phase plate from FEI is not available as a external scripting call.  Ways around this lack of feature has been developed using simulated mouse manipulation scripting from AutoIt.  There are a number of workflow modification to achieve automated single-particle imaging that involves patch position advancing at user-defined number of exposures, charging the phase plate to a stable phase shift value, and multiple target beam-tilt focusing.

[[Volta Phase Plate Usage]]

[[Phase Plate Aligner Node Class]]

[[Special Beam Tilt Calibration for Phase Plate]]

[[MSI-PP Appplication]]

[[How often should the phase plate moved to the next patch ?]]

[[Leginon "MSI-T-Tilt" Application]]

[[Slack notification for Leginon errors]]

h2. General Features

1. Target Finder:

1a. Option to force user to add focus target: This feature is default to require focus targets but can be set to "Do not require focus targets in user verification" in advanced settings dialog in any Target Finder.

1b. Multiple Hole Template generation.

1c. Using Focus hole selection option with an offset.  Useful when the edge of the hole is needed to perform autofocusing.

1d. Option to define minimal hole stats standard deviation.

1e. Red square next to the node name Indicates that settings chosen by the user currently are such that tree-depth traversal automated data collection would be hindered.  For example, "Allow user verification" is turned on.

2. Refinement of the behavior of Reference nodes such as "Align ZLP"

2a. Add a reference target from a Reference Node at the center of the image acquired that can be more accurately moved to with iterative move by Navigator. (Need to use new MSI applications).

2b. Set settle time after Leginon is moved back from the reference target.

3. Enforce dark current image acquisition.

3a. Automatically acquire and update hardware dark current image on K2 camera while "N2 filling" is running.

3b. Automatically acquire and update hardware dark current image on K2 camera for acquiring Bright reference image.

4. Some TEM remote control in Leginon (in development) (Need to use new MSI applications)

5. Tomography

5a. Aternating tilt sequence

5b. Option to use the preset exposure time at all tilts and thus ignore dose adjustment.

6. Focuser

6a. Option to use diagonal beam tilts for phase plate data collection to minimize charging of unused phase plate patch.

6b. Not to recheck drift until it passes at first time. Such was the default behavior but tend to delay stabilization since the first measurement always shows higher drift from beam induced movement.

7. Stage alpha tilt stability enforcement.  This is added because the goniometers on some scope slips in the way that the position reached is always larger than the requested angle, causing the tilt angle drifts over time.  The stage tilt is enforced in

* Grid Targeting Node Settings

* Turn on the advanced settings "Tilt the stage like its parent image" in all Acquisition node class if the tilt needs to be preserved.

8. Presets Manager

* General time out and error notification with Slack

9. Image rotation and scale modification calibrations - For highly defocused image that has introduced rotation and size change of the image.