Topics

Messages in this system are sent and received using our Pigeon library. The message definitions for each topic are listed below, and implemented in the library linked above. These are also available on the Python package index as pigeon-tem-comms.

buffer.status
calibration.centroid
calibration.resolution
camera.command
camera.image
camera.settings
camera.status
montage.complete
montage.minimaps
qc.status
roi.create
roi.current
roi.load
scope.command
scope.status
stage.aperture.command
stage.aperture.status
stage.motion.command
stage.motion.status
stage.rotation.command
stage.rotation.status
state
tile.mini
tile.preview
tile.processed
tile.raw
tile.statistics.focus
tile.statistics.histogram
tile.statistics.min_max_mean
tile.transform
ui.edit
ui.run
ui.setup

buffer.status

Properties

queue_length (integer, required)
free_space (integer, required)
upload_rate (integer, required)

Sender

Tile Upload Buffer

Receivers

User Interface

calibration.centroid

Properties

aperture_id (integer, required)
x (integer, required)
y (integer, required)

Sender

Receivers

calibration.resolution

Properties

lowmag (object, required): Can contain additional properties.
- Additional properties: Refer to _Resolution.
mag (object, required): Can contain additional properties.
- Additional properties: Refer to _Resolution.

Definitions

_Resolution (object): Cannot contain additional properties.
- nm_per_px (array, required): Length must be equal to 2.
- rotation (number, required)

Sender

Receivers

camera.command

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
brightfield: Default: false.
- Any of
  - boolean
  - null
darkfield: Default: false.
- Any of
  - boolean
  - null
lens_correction: Default: true.
- Any of
  - boolean
  - null

Sender

pyTEM

Receivers

Camera Service

camera.image

Properties

tile_id (string, required)
montage_id (string, required)

Sender

Camera Service

Receivers

pyTEM

camera.settings

Properties

exposure: Default: null.
- Any of
  - number
  - null
gain: Default: null.
- Any of
  - number
  - null
width: Default: null.
- Any of
  - integer
  - null
height: Default: null.
- Any of
  - integer
  - null

Sender

pyTEM

Receivers

Camera Service

camera.status

Properties

exposure (number, required)
gain (number, required)
width (integer, required)
height (integer, required)
temp (number, required)
target_temp (number, required)
device_name (string, required)
device_model_id (integer, required)
device_sn (string, required)
bit_depth
- Any of
  - integer
  - string

Sender

Camera Service

Receivers

montage.complete

Properties

montage_id (string, required)
tiles (object, required): Can contain additional properties.
- Additional properties: Refer to Tile.
acquisition_id (string, required)
start_time (string, format: date-time, required)
pixel_size (number, required)
rotation_angle (number, required)
aperture_centroid (array, required): Length must be equal to 2.

Definitions

Tile (object): Cannot contain additional properties.
- raster_index (integer, required)
- stage_position (array, required): Length must be equal to 2.
- raster_position (array, required): Length must be equal to 2.

Sender

Receivers

montage.minimaps

Properties

montage_id (string, required)
montage (required): Refer to Minimap.
focus (required): Refer to Minimap.

Definitions

Minimap (object): Cannot contain additional properties.
- image
  - Any of
    - string
    - null
- colorbar (string, required)
- min
  - Any of
    - number
    - null
- max
  - Any of
    - number
    - null

Sender

Receivers

qc.status

Properties

state (string, required): Must be one of: “GOOD”, “STOP_AT_END”, or “STOP_NOW”.

Sender

QC Service

Receivers

pyTEM

roi.create

Properties

center (required): Refer to Vertex.
width (number, required)
height (number, required)
rotation_angle (number): Default: 0.0.
montage_id (string, required)
specimen_id: Default: null.
- Any of
  - string
  - null
grid_id: Default: null.
- Any of
  - string
  - null
section_id: Default: null.
- Any of
  - string
  - null
queue_position: Position in queue, None means set as current. Default: null.
- Any of
  - integer
  - null

Definitions

Vertex (object): Cannot contain additional properties.
- x (number, required)
- y (number, required)

Sender

Receivers

roi.current

Properties

vertices (array, required)
- Items: Refer to Vertex.
rotation_angle (number, required)
buffer_size (number): Default: 0.0.
montage_id (string, required)
specimen_id: Default: null.
- Any of
  - string
  - null
grid_id: Default: null.
- Any of
  - string
  - null
section_id: Default: null.
- Any of
  - string
  - null
metadata: Default: null.
- Any of
  - object: Can contain additional properties.
  - null
queue_position: Position in queue, None means set as current. Default: null.
- Any of
  - integer
  - null

Definitions

Vertex (object): Cannot contain additional properties.
- x (number, required)
- y (number, required)

Sender

Receivers

roi.load

Properties

specimen_id (string, required)
section_id (string, required)
grid_id: Default: null.
- Any of
  - string
  - null
queue_position: Position in queue, None means set as current. Default: null.
- Any of
  - integer
  - null

Sender

Receivers

scope.command

Properties

focus: Default: null.
- Any of
  - integer
  - null
mag_mode: Default: null.
- Any of
  - string: Must be one of: “LM”, “MAG1”, or “MAG2”.
  - null
mag: Default: null.
- Any of
  - integer
  - null
brightness: Default: null.
- Any of
  - integer
  - null
beam_offset: Default: null.
- Any of
  - array: Length must be equal to 2.
  - null
spot_size: Default: null.
- Any of
  - integer
  - null
screen: Default: null.
- Any of
  - string: Must be one of: “up” or “down”.
  - null

Sender

pyTEM

Receivers

Microscope Service

scope.status

Properties

focus (integer, required)
aperture
- Any of
  - string
  - null
mag_mode (string, required): Must be one of: “MAG” or “LOWMAG”.
mag (integer, required)
tank_voltage (integer, required)
brightness (integer, required)
beam_offset (array, required): Length must be equal to 2.
spot_size (integer, required)
screen
- Any of
  - string: Must be one of: “up” or “down”.
  - null

Sender

Microscope Service

Receivers

stage.aperture.command

Properties

aperture_id: Default: null.
- Any of
  - integer
  - null
calibrate (boolean): Default: false.

Sender

pyTEM

Receivers

Stage Service

stage.aperture.status

Properties

current_aperture
- Any of
  - integer
  - null
calibrated (boolean, required)
error (string): Default: "".

Sender

Stage Service

Receivers

stage.motion.command

Properties

x: Default: null.
- Any of
  - integer
  - null
y: Default: null.
- Any of
  - integer
  - null
z: Default: null.
- Any of
  - integer
  - null
calibrate (boolean): Default: false.

Sender

pyTEM

Receivers

Stage Service

stage.motion.status

Properties

x
- Any of
  - integer
  - null
y
- Any of
  - integer
  - null
z: Default: null.
- Any of
  - integer
  - null
in_motion (boolean, required)
error (string): Default: "".

Sender

Stage Service

Receivers

stage.rotation.command

Properties

angle_x: Default: null.
- Any of
  - number
  - null
angle_y: Default: null.
- Any of
  - number
  - null
eucentric_height: Default: null.
- Any of
  - number
  - null
calibrate (boolean): Default: false.

Sender

pyTEM

Receivers

stage.rotation.status

Properties

angle_x (number, required)
angle_y (number, required)
eucentric_height (number, required)
in_motion (boolean, required)
error (string): Default: "".

Sender

Receivers

state

Properties

state (string, required)

Sender

Receivers

tile.mini

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
image (string, required)

Sender

Receivers

tile.preview

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
image (string, required)

Sender

Receivers

tile.processed

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
path (string, required)

Sender

Image Processing Pipeline

Receivers

Tile Upload Buffer

tile.raw

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
path (string, required)

Sender

pyTEM

Receivers

Image Processing Pipeline

tile.statistics.focus

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
focus (number, required)

Sender

Image Processing Pipeline

Receivers

tile.statistics.histogram

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
hist (array, required)
- Items (integer)

Sender

Image Processing Pipeline

Receivers

tile.statistics.min_max_mean

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
min (integer, required)
max (integer, required)
mean (integer, required)
std (integer, required)

Sender

Image Processing Pipeline

Receivers

tile.transform

Properties

tile_id (string, required)
montage_id (string, required)
row (integer, required)
column (integer, required)
overlap (integer, required)
rotation (number, required)
x (number, required)
y (number, required)

Sender

Image Processing Pipeline

Receivers

ui.edit

Properties

roi_id (string, required)
roi_pos_x (integer, required)
roi_pox_y (integer, required)
roi_width (integer, required)
roi_height (integer, required)
roi_angle (number, required)

Sender

User Interface

Receivers

ui.run

Properties

session_id: Default: null.
- Any of
  - string
  - null
grid_first: Default: null.
- Any of
  - integer
  - null
grid_last: Default: null.
- Any of
  - integer
  - null
montage (boolean): Default: false.
abort_now (boolean): Default: false.
abort_at_end (boolean): Default: false.
resume (boolean): Default: false.
cancel (boolean): Default: false.

Sender

User Interface

Receivers

ui.setup

Properties

conch_owner: Default: null.
- Any of
  - string
  - null
auto_focus (boolean): Default: false.
auto_exposure (boolean): Default: false.
lens_correction (boolean): Default: false.
acquire_brightfield (boolean): Default: false.
acquire_darkfield (boolean): Default: false.
center_beam (boolean): Default: false.
spread_beam (boolean): Default: false.
find_aperture (boolean): Default: false.
calibrate_resolution (boolean): Default: false.
grid: Default: null.
- Any of
  - integer
  - null
mag_mode: Default: null.
- Any of
  - string: Must be one of: “LM”, “MAG1”, or “MAG2”.
  - null
mag: Default: null.
- Any of
  - integer
  - null

Sender

User Interface