pyTEM is the main hierarchical state machine orchestrating all the components. This service uses the Pigeon client for communication via the message broker. Furthermore, a library integrating Pigeon and the Python Transitions library to allow easy creation of the state machine. This library can also create a state transition diagrams of the state machine:

Simplified State Diagram

A simplified version of this schematic is:

Below, the functionality of each of “states” shown above is detailed. In reality, each of these “states” is a state machine in and of itself.

Preview

The Preview machine is used for previewing the image data, and checking that the microscope functions as expected.

Acquisition

The Acquisition machine is used to set up and capture a montage.

Montage

The Montage machine collects the required tiles.

UpdateImage

The UpdateImage machine requests an image from the camera, and sends it to the image processing pipeline. Ultimately, this image will then be shown on the UI.

Darkfield

The Darkfield machine collects a darkfield image by lowering the screen on the microcope, collecting a series of images, averaging them, then raising the screen again.

Brightfield

The Brightfield machine collects a brightfield image by moving the stage while collecting a series of images, then averaging them.

AutoFocus

The AutoFocus machine optimizes the focus by maximizing the focus score produced by the image processing pipeline.

AutoExposure

The AutoExposure machine optimizes the exposure by finding the camera exposure which produces a mean value within the correct range as calculated by the image processing pipeline.

BeamCenter

The BeamCenter machine centers the electron beam in the microscope’s field of view.

BeamSpread

The BeamSpread machine spreads the beam to get an even density of electrons over the field of view.

ChangeAperture

The ChangeAperture machine changes the current aperture of the tape or stick that is being imaged.

LensCorrection

The LensCorrection machine collects a lens correction montage.

FindAperture

The FindAperture machine finds the bounds of the current aperture by moving the stage and processing images.

MoveStage

The MoveStage machine moves the stage to the location of the next tile.

CaptureTile

The CaptureTile machine captures a single tile using the camera.

Shutdown

In the Shutdown machine, the microscope is placed into a safe state. Ideally, the beam is turned off, and the screen is lowered.

Note:

Historically, orchestration of all components was accomplished using pytemca documented here.