Microscope Commands Documentation

Microscope Control Software version 2.2.2.0

JSON command protocol
TCP/IP port: 16951
Message format: message length (4 bytes, int32) followed by JSON message

Field	Type/Value	Description	Required	Default
Common for all components
Ping	command	Ping to check that component is able to receive commands.
	response

Common	command	Represent a command that can be executed on a source.
ComponentName	string	Name of the component to which command is addressed.	Yes
CommandName	string	Name of the command.	Yes
	response
Success	bool	Indicates if command was successful.	Yes
ErrorMessage	string	Error message describing command error.	Yes
Time	double?	Time in ms it took to execute command or null if unknown.	Yes

Common for all devices
Connect	command	Connect microscope to the device.
	response

Disconnect	command	Disconnect microscope from device.
	response

Ping	command	Ping to check that component is able to receive commands.
	response

WaitReady	command	Wait for a device to be ready.
	response

AcquisitionControllerDevice
LaserAblateUV	command	Trigger a series of pulses of UV ablation laser.
PulseCount	int	Number of pulses to trigger.	Yes
	response

Acquire	command	Generate acquisition controller signals.
IlluminationSettings	string	Name of the illumination settings to use.	Yes
ExposureSettings	string	Name of the exposure settings to use.	Yes
	response

CameraDevice
DisplayedViewSet	command	Set the displayed view in image viewer.
View	int	The index of the view to display, one based.	Yes
	response

ImageInfoGet	command	Get info on imaging setup.
	response
Width	int	Width of the image in pixels.	Yes
Height	int	Height of the image in pixels.	Yes
Planes	int	Number of planes.	Yes
Channels	int	Number of channels.	Yes
Views	int	Number of views.	Yes
Position	string	Name of position (or null if not known).	Yes
Settings	string	Name of settings.	Yes
TimePoint	int?	Time point starting at 1.	Yes
VoxelX	double?	Size of Voxel X in um.	Yes
VoxelY	double?	Size of Voxel Y in um.	Yes
VoxelZ	double?	Size of Voxel Z in um (or null if no stack).	Yes
NumericalAperture	double	Numerical aperture of objective.	Yes

OffsetGet	command	Get offset between camera views.
	response
OffsetX	int	The offset between views along X-axis.	Yes
OffsetY	int	The offset between views along Y-axis.	Yes

OffsetSet	command	Set the offset between camera views.
OffsetX	int	The offset between views along X-axis.	Yes
OffsetY	int	The offset between views along Y-axis.	Yes
	response

ImageGet	command	Get image from the camera buffer.
Plane	int	Plane to get (1 based).	No	1
ChannelIndex	int	Index of channel to get (1 based).	No	1
ViewIndex	int	Index of View to get (1 based).	No	1
Top	int?	Index of top most pixel to get (0 based), null to center.	No	null
Left	int?	Index of left most pixel to get (0 based), null to center.	No	null
Width	int?	Width of the image in pixels or null to get full width.	No	null
Height	int?	Height of the image in pixels or null to get full height.	No	null
	response
Width	int	Width of the image.	Yes
Height	int	Height of the image.	Yes
ImageData	string	Image data represented in base64 encoding.	Yes

FilterWheelDevice
Move	command	Move filter wheel to specified filter.
FilterName	string	Name of the filter settings to move device to.	Yes
Force	bool	Whether to force the filter wheel to move (even if already at correct position).	No	false
	response

MoveTo	command	Move filter wheel to specified position.
Position	int	Position to move the device to.	Yes
Force	bool	Whether to force the filter wheel to move (even if already at correct position).	No	false
	response

IlluminationModuleDevice
CurrentIlluminationGet	command	Get values currently applied on the hardware.
	response
Name	string	Name of illumination settings.	Yes
TranslationX	double	The translation along X-axis.	Yes
RotationX	double	The rotation along X-axis.	Yes
TranslationY	double	The translation along Y-axis.	Yes
TranslationZ	double	The translation along Z-axis.	Yes
RotationZ	double	The rotation along Z-axis.	Yes

IlluminationSet	command	Set the illumination settings.
Name	string	Name of the illumination settings to set.	Yes
TranslationX	double?	The translation along X-axis or null to keep original value.	No	null
RotationX	double?	The rotation along X-axis or null to keep original value.	No	null
TranslationY	double?	The translation along Y-axis or null to keep original value.	No	null
TranslationZ	double?	The translation along Z-axis or null to keep original value.	No	null
RotationZ	double?	The rotation along Z-axis or null to keep original value.	No	null
SetDevice	bool	Whether to apply the new settings on device.	No	false
	response

OffsetBaseGet	command	Get base offset values.
	response

PositionAlignmentSet	command	Set position specific Z-alignment and enable the position.
Name	string	Name of the position alignment settings to set.	Yes
TranslationZ	double?	Translation along Z-axis to set or null to keep original value.	No	null
Enable	bool?	Enable to set or null to keep original value.	No	null
	response

PositionAlignmentGet	command	Get position specific Z-alignment.
Name	string	Name of the position alignment settings to get.	Yes
	response
Name	string	Name of the position.	Yes
TranslationZ	double	Translation along Z-axis.	Yes
Enable	bool	Whether the alignment is applied.	Yes

OffsetsBaseSet	command	Set base offsets, all current settings are overwritten.
OffsetsBase	list of dict	The list of base offsets. Keys of dict listed below.	Yes
Branch	int	Unique number of illumination branch (value 1, 2 or 3).	Yes
Scanner1Offset	double	Voltage on scanner 1.	Yes
Scanner2Offset	double	Voltage on scanner 2.	Yes
Scanner3Offset	double	Voltage on scanner 3.	Yes
Scanner4Offset	double	Voltage on scanner 4.	Yes
	response

IlluminationGet	command	Get current illumination settings.
Name	string	Name of the illumination settings to get.	Yes
	response
Name	string	Name of illumination settings.	Yes
TranslationX	double	The translation along X-axis.	Yes
RotationX	double	The rotation along X-axis.	Yes
TranslationY	double	The translation along Y-axis.	Yes
TranslationZ	double	The translation along Z-axis.	Yes
RotationZ	double	The rotation along Z-axis.	Yes

System
GetDeviceList	command	Get a list of names and types of devices connected to the microscope.
	response
DeviceNames	list of string	List of device names.	Yes
DeviceTypes	list of string	List of device types.	Yes

GetDeviceType	command	Get the type of a device.
QueryDeviceName	string	The name of the device to get the type for.	Yes
	response
DeviceType	string	Type of the device.	Yes

PhotomanipulationComponent
OffsetsBaseGet	command	Get base offset values from internal or external photomanipulation laser.
OffsetsInternal	bool	Whether offsets are from internal or external photomanipulation laser.	No	true
	response
OffsetsBase	dict	The base offsets. Keys of dict listed below.	Yes
Scanner1Offset	double	Voltage on scanner 1 (closest to scan lens).	Yes
Scanner2Offset	double	Voltage on scanner 2.	Yes
Scanner3Offset	double	Voltage on scanner 3.	Yes
Scanner4Offset	double	Voltage on scanner 4 (furthest from scan lens).	Yes

OffsetsBaseSet	command	Set base offsets for internal or external photomanipulation laser, all current settings are overwritten.
OffsetsBase	dict	The baser offsets. Keys of dict listed below.	Yes
Scanner1Offset	double	Voltage on scanner 1 (closest to scan lens).	Yes
Scanner2Offset	double	Voltage on scanner 2.	Yes
Scanner3Offset	double	Voltage on scanner 3.	Yes
Scanner4Offset	double	Voltage on scanner 4 (furthest from scan lens).	Yes
	response

StageXYZDevice
ForgetCurrentPosition	command	Make stage forget position name on which it's located.
	response

GetZStack	command	Get Z-Stack settings.
Name	string	Name of the Z-Stack settings.	Yes
	response
Name	string	Name of the Z-Stack settings.	Yes
Step	double	The step size in micrometer between each plane.	Yes
Planes	int	The number of planes of the stack.	Yes

GetZStackNames	command	Get a list of Z-Stack settings names.
	response
Names	list of string	List of Z-Stack names.	Yes

Move	command	Move stage to a position.
Name	string	Name of the position settings.	Yes
ZStackName	string	Name of the Z-stack settings to use or null to move to center.	No	null
Plane	int?	Plane of the Z-stack to move to or null to move to center.	No	null
Offset	list of double	List of relative X, Y, Z offsets to add to the position.	No	null
	response

PositionNamesGet	command	Get a list of position names.
	response
Names	list of string	List of position names.	Yes

PositionSet	command	Set position settings.
Name	string	Name of the position settings to set.	Yes
NewName	string	The new name of the position settings or null to keep original value.	No	null
PositionX	double?	Position on X-axis to set or null to keep original value.	No	null
PositionY	double?	Position on Y-axis to set or null to keep original value.	No	null
PositionZ	double?	Position on Z-axis to set or null to keep original value.	No	null
SkipPosition	bool?	Whether to skip the position or null to keep original value.	No	null
	response

PositionGet	command	Get position settings.
Name	string	Name of the position settings.	Yes
	response
Name	string	Name of the position.	Yes
PositionX	double	Position on X-axis.	Yes
PositionY	double	Position on Y-axis.	Yes
PositionZ	double	Position on Z-axis.	Yes
SkipPosition	bool	Whether the position is skipped.	Yes

SetZStack	command	Set Z-Stack settings.
Name	string	Name of the Z-stack settings to set.	Yes
NewName	string	The new name of the Z-stack settings or null to keep original value.	No	null
Step	double?	The step size in micrometer between each plane to set or null to keep original value.	No	null
Planes	int?	The number of planes of the stack to set or null to keep original value.	No	null
	response

TimeLapseController
ContinueFromPause	command	Continue from pause after a position.
	response

GetAcquisitionSettings	command	Get acquisition settings.
	response
TimeInterval	double	The time interval in seconds between two time points.	Yes
Repetitions	int	The number of time points to acquire.	Yes
ExperimentName	string	The name of the experiment.	Yes

GetChannelSettings	command	Get the channel settings in a settings profile.
SettingsProfile	string	The name of the settings profile to get the channel settings from.	Yes
Name	string	The name of the channel settings to get.	Yes
	response
Name	string	The name of the channel settings.	Yes
Enabled	bool	Whether the channel should be acquired.	Yes
AcquireNthTimePoint	int	Interval at which the channel should be acquired. It is acquired at every specified number of time points.	Yes
Color	enum	The channel default color. Possible values listed below.	Yes
Red	string	Red color.	-
Green	string	Green color.	-
Blue	string	Blue color.	-
Cyan	string	Cyan color.	-
Magenta	string	Magenta color.	-
Yellow	string	Yellow color.	-
White	string	White color.	-
Illumination	string	The name of the illumination settings to apply on acquisition controller device.	Yes
Exposure	string	The name of the exposure settings to apply on acquisition controller device.	Yes

GetChannelSettingsNames	command	Get the list of channel settings names in a settings profile.
SettingsProfile	string	The name of the settings profile to get the channel settings names from.	Yes
	response
Names	list of string	List of channel settings names.	Yes

GetSettingsProfile	command	Get a settings profile.
Name	string	The name of the settings profile to get.	Yes
	response
Name	string	The name of the settings profile.	Yes
Enabled	bool	Whether the settings profile should be acquired.	Yes
ZStack	string	The name of the Z-Stack settings to apply, single plane if null.	Yes
Positions	list of string	The list of positions to acquire. If null, all positions are acquired. If empty, no positions are acquired.	Yes
Views	enum	The view(s) to acquire. Possible values listed below.	Yes
View1	string	View 1	-
View2	string	View 2	-
View1and2	string	View 1 and 2	-

GetSettingsProfileNames	command	Get the list of settings profile names.
	response
Names	list of string	List of settings profile names.	Yes

NoPauseAfterPosition	command	Disable pause after every position has been acquired.
	response

PauseAfterPosition	command	Ask time-lapse to pause after each position has been acquired.
	response

SetAcquisitionSettings	command	Set acquisition settings.
TimeInterval	double?	The time interval in seconds between two time points to set or null to keep original value.	No	null
Repetitions	int?	The number of time points to acquire to set or null to keep original value.	No	null
ExperimentName	string	The name of the experiment to set or null to keep original value.	No	null
	response

SetChannelSettings	command	Set the channel settings in a settings profile.
SettingsProfile	string	The name of the settings profile to set the channel settings in.	Yes
Name	string	Name of the channel settings to set.	Yes
NewName	string	The new name of the settings profile or null to keep original value.	No	null
Enabled	bool?	Whether the channel settings should be acquired or null to keep original value.	No	null
AcquireNthTimePoint	int?	Interval at which the channel should be acquired or null to keep original value.	No	null
Color	enum?	The channel default color or null to keep original value. Possible values listed below.	No	null
Red	string	Red color.	-
Green	string	Green color.	-
Blue	string	Blue color.	-
Cyan	string	Cyan color.	-
Magenta	string	Magenta color.	-
Yellow	string	Yellow color.	-
White	string	White color.	-
Illumination	string	The name of the illumination settings to apply or null to keep original value.	No	null
Exposure	string	The name of the exposure settings to apply or null to keep original value.	No	null
	response

SetSettingsProfile	command	Set a settings profile.
Name	string	Name of the settings profile to set.	Yes
NewName	string	The new name of the settings profile or null to keep original value.	No	null
Enabled	bool?	Whether the settings profile should be acquired or null to keep original value.	No	null
ZStack	string	The name of the Z-Stack settings to apply or null to keep original value.	No	null
IsSinglePlane	bool?	Whether the settings profile should be acquired in single plane or null to keep original value. If false, must be defined. If true, must be null.	No	null
Positions	list of string	The list of positions to acquire or null to keep original value.	No	null
PositionsAll	bool?	Whether all positions should be acquired or null to keep original value. If true, must be null. If false, must be defined.	No	null
Views	enum?	The view(s) to acquire or null to keep original value. Possible values listed below.	No	null
View1	string	View 1	-
View2	string	View 2	-
View1and2	string	View 1 and 2	-
	response

Start	command	Start a time-lapse.
	response

Stop	command	Stop time-lapse.
	response

WaitForPause	command	Wait until time-lapse controller is paused after a position.
Timeout	int	Waiting timeout in ms, -1 to wait indefinitely.	No	-1
	response
Position	string	Position which was paused.	Yes
TimePoint	int	Time point which was paused.	Yes
Timeout	bool	True if timeout, if paused false	Yes

Snap	command	Snap an image.
Illumination1	bool?	If not null override user settings and enable or disable illumination 1.	No	null
Illumination2	bool?	If not null override user settings and enable or disable illumination 2.	No	null
Fast	bool	Whether to bypass setting of settable devices (for example filter wheels will not move to defined settings).	No	false
	response