Leginon

h1. Continuous tilt electron diffraction recording use Ceta or Ceta-D camera and TFS scopes

Micro-ED involves recording 3D crystal electron diffraction pattern during a continuous stage tilt.  Leginon implementation of this application includes the listed components below and is available by using myami-ed branch until it is officially added to future release.  As is, it is only fully implemented for TFS Ceta or Ceta-D camera.

Since many of the feature required here are not available through Standard or Advanced TEM Scripting from TFS, AutoIt scripts are used in several places.

h2. Components of the feature

# Diffraction mode TEM instrument

# Beamstop control: achieved by AutoIt Scripts BeamstopIn and BeamstopOut

# Rolling-shutter movie acquisition using TIA interface

# Data conversion and upload of the movies into Leginon database and crystallography format

# [[ MSI-Diffr application ]]

# [[Camera length calibration]]

h2. Installation (assuming that you've already have Leginon installation).

# Check that you have access to Advanced TEM Scripting (frame-saving upgrade not needed).

# Install or set environment to use git branch myami-ed or current myami-beta on TFS microscope with Ceta camera as well as your leginon linux box.

# import updated Calibrations application (see [[Steps_involved_in_the_installation]])

# import MSI-diffraction  and settings from your_myami/leginon/applications (see general description of [[Steps_involved_in_the_installation]] regarding importing application and additional settings for the application)

# [[Setup Diffraction mode TEM instrument]]

# [[Setup Ceta to use Advanced TEM Scripting]]

# [[AutoIt program and script compilation]]

h2. Usage

h3.  Confirm that instruments.cfg is properly set up to use feicam for Ceta camera.  Especially if you use Falcon camera on the same instrument for imaging.

h3. Start MSI-DIffr application and assign client as required.

h3. Setup df preset

h4. Microscope setup for df preset

1. Center the beam and set in nanoprobe parallel illumication and eucentric focus in SA range imaging mode.

2. Change spot size to larger number such as spot 10 and center this beam is needed through Direct Alignment reset Beam Shift.

3. Change gun lens to get much weaker beam. For example from 3.3 to 7.1 reduces the beam current to 25%.  You probably won't be able to see the beam any more on the flucam.

4. Push the diffraction button on the control panel to put this in diffraction mode.

5. Select desired camera length

6. Push the eucentric button on the control panel to focus the beam on the diffraction plane.

7. Insert beam stop and center the diffraction beam behind it.

h4. Camera setup for df preset

dimension: 2048 x 2048

binning: 2 x 2

exposure time: 1000 ms (not used during movie collection, but used for DPreview node)

h4. Cycle through hl and df presets a few times to allow it to settle on lens normalization before adjusting df preset diffraction shift again.  Repeat until satisfied.