acquifer.core

Class TcpIp

Object

acquifer.core.TcpIp

public class TcpIp
extends Object

Class implementing remote control of the IM via TcpIp.
The TcpIp protocol is implemented between an external program (ex: python/Fiji script) and the control software of the image machine, to exchange commands and receiving feedback.
Potential applications include getting feedback on the IM state, running custom acquisition, moving IM axis (X/Y/Z/objective/channels/filters)...
See examples of how to use this Java API in Fiji (the same TcpIp commands apply to any another java application).

Requirements
The Imaging Machine GUI must be opened to be able to exchange TcpIp commands, and the "Block remote access" option in the service panel deactivated (restart of the software needed to take effect).

If the access is enabled, the beginning of the Log should contain a line such as
[09:48:34:102] inf|SmartImaging IP Server started on port 6200

Note : Access to the service panel is protected by a password. Contact your system administrator or the acquifer support team to activate the option for you.

The TCPIP communication protocol of the IM software relies on IPv6, with the following IP "::1" (localhost).
By default, it uses the port 6200, but a custom port number can be specified in the service panel. In this case, the TcpIp constructor below should use this custom port number.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TcpIp.ControllerMode
static class	TcpIp.FilenameMetadata
static class	TcpIp.GoToMode

Constructor Summary

Constructors

Constructor and Description
TcpIp() Open the TcpIp connection on localhost, and default Port 6200.
TcpIp(int port) Open the TcpIp connection to the Imaging Machine (localhost), with custom port.

Method Summary

Modifier and Type	Method and Description
String	acquireVideo(int channelNumber, int objective, String lightSource, int detectionFilter, int intensity, int exposure, double zPosition, int nFrames) Same as acquireVideo(int, int, String, int, int, int, double, int, boolean, String) using default project folder for the image directory and lightConstantOn to false.
String	acquireVideo(int channelNumber, int objective, String lightSource, int detectionFilter, int intensity, int exposure, double zPosition, int nFrames, boolean lightConstantOn, String saveDirectory) Acquire a short video of nFrames at the current XY position and given Z-position.
String	acquireZstack(int channelNumber, int objective, String lightSource, int detectionFilter, int intensity, int exposure, double zStackCenter, int nSlices, double zStepSize) Similar to acquireZstack(int, int, String, int, int, int, double, int, double, boolean, String), but using the default project folder/plateID for the image directory and the light-source blinking (lightConstantOn to false).
String	acquireZstack(int channelNumber, int objective, String lightSource, int detectionFilter, int intensity, int exposure, double zStackCenter, int nSlices, double zStepSize, boolean lightConstantOn, String saveDirectory) Acquire at the current XY-position, a Z-stack composed of nSlices, distributed evenly around a Z-centre position, using current camera settings.
void	closeConnection() Close the tcpip connection, no more commands can be sent to the IM with this object after that.
void	closeLid()
static double[]	convertXYpixelToMillimeters(int x, int y, String imageName, int width, int height) Convert from pixel coordinates in an image to the corresponding objective axis-coordinates of the imaging machine.
TcpIp.ControllerMode	getMode() Return the current controller mode (LIVE/SCRIPT).
String	getModeAsString() Return the current controller mode (LIVE/SCRIPT) as a upper-case string.
int	getNumberOfColumns() Return the number of plate columns.
int	getNumberOfRows() Return the number of plate rows.
int	getObjectiveIndex() Return the currently selected objective-index (1 to 4).
double	getPositionX() Return the current objective x-axis position in mm.
double	getPositionY() Return the current objective y-axis position in mm.
double	getPositionZ() Return the current objective z-axis position in µm.
double	getTemperatureAmbient() Get the current ambient temperature (°C).
double	getTemperatureSample() Get the current sample temperature (°C).
double	getTemperatureTarget() Get the temperature set as target (°C).
boolean	isLidClosed()
boolean	isLidOpened()
boolean	isLiveMode() Check if currently in live mode.
boolean	isScriptMode() Check if currently in script mode.
boolean	isTemperatureRegulated()
void	log(String message) Log a message to display in the imgui log.
void	moveXYby(double x, double y) Move x,y by a given step-size (mode Relative), in mm with 0.001 decimal precision.
void	moveXYto(double x, double y) Move x,y to target position (mode Absolute), in mm with 0.001 decimal precision.
void	moveXYto(acquifer.core.WellPosition wellPosition) Move x,y to a specific well position and update current well/subposition metadata.
void	moveXYZto(double x, double y, double z) Move to x,y position (mm, 0.001 precision) and z-position in µm (0.1 precision).
void	moveZby(double z) Move Z-position by given step size (mode Relative), in µm with 0.1 precision.
void	moveZto(double z) Move Z-position to target position (mode Absolute), in µm with 0.1 precision.
void	openLid()
void	resetCamera() Reset camera to full-size field of view (2048x2048 pixels) and no binning.
double	runHardwareAutoFocus(int objective, int detectionFilter, double zStart, double calibrationOffset) Run a hardware autofocus and return the Z-position found.
void	runScript(String scriptPath) Start a .imsf or .cs script to run an acquisition.
double	runSoftwareAutoFocus(int objective, String lightSource, int detectionFilter, int intensity, int exposure, double zStackCenter, int nSlices, double zStepSize) Same as runSoftwareAutoFocus(int, String, int, int, int, double, int, double, boolean) with lightConstantOn default to false.
double	runSoftwareAutoFocus(int objective, String lightSource, int detectionFilter, int intensity, int exposure, double zStackCenter, int nSlices, double zStepSize, boolean lightConstantOn) Run a software autofocus with a custom channel and current objective and camera settings.
void	setBrightField(int channelNumber, int detectionFilter, int intensity, int exposure) Same as setBrightField(int, int, int, int, boolean) with default lightConstantOn to false (ie light-source is synchronised with the camera/blinking).
void	setBrightField(int channelNumber, int detectionFilter, int intensity, int exposure, boolean lightConstantOn) Activate the brightfield light lightSource.
void	setBrightFieldOff() Switch-off the brightfield channel if in live-mode, by setting intensity and exposure time to 0.
void	setCamera(int x, int y, int width, int height) Set the fraction of the camera sensor used for the next acquisition, also reset binning to default (1=no binning).
void	setCamera(int x, int y, int width, int height, int binning) Set camera acquisition settings such as sensor area used for acquisition and binning factor.
void	setCameraBinning(int binning) Set the binning factor (1,2 or 4), also reset the camera sensor area to full-frame (2048x2048).
void	setDefaultProjectFolder(String folder) Set the default project folder, used when no path is specified for the acquire command.
void	setFluoChannel(int channelNumber, String lightSource, int detectionFilter, int intensity, int exposure) Same as setFluoChannel(int, String, int, int, int, boolean) with default lightConstantOn to false (ie light-source is synchronised with the camera/blinking).
void	setFluoChannel(int channelNumber, String lightSource, int detectionFilter, int intensity, int exposure, boolean lightConstantOn) Activate one or multiple LED light sources for fluorescence imaging.
void	setFluoChannelOff() Switch off all the LED light sources (fluorescence) by setting the intensities to 0%.
void	setLightSource(int channelNumber, String lightSource, int detectionFilter, int intensity, int exposure) Same as setLightSource but with default lightConstantOn to false.
void	setLightSource(int channelNumber, String lightSource, int detectionFilter, int intensity, int exposure, boolean lightConstantOn) Switch-on light source, brightfield or fluorescent one(s).
void	setLightSourceOff(String lightSource) Switch-off a light-source (brightfield or fluo).
void	setMetadata(String wellId, int wellNumber, int subposition, int timepoint) Update multiple metadata at once, used to name image files for the next acquisition(s).
void	setMetadataChannel(int channel) Update the channel metadata used to name the image files for the next acquisitions (CO tag).
void	setMetadataSubposition(int subposition) Update the well subposition index (within a given well), used to name the image files for the next acquisitions (PO tag).
void	setMetadataTimepoint(int timepoint) Update the timepoint (or loop iteration) index, used to name the image files for the next acquisitions (LO tag).
void	setMetadataWellId(String wellID) Update the well ID (ex: "A001") using the default leading character '-' for compatibility with Acquifer software suite.
void	setMetadataWellId(String wellID, char leadingChar) Update the well ID (ex: "A001"), used to name the image files for the next acquisitions.
void	setMetadataWellNumber(int number)
void	setMode(String mode) Alias for setMode(ControllerMode) using "script" or "live" for the mode.
void	setMode(TcpIp.ControllerMode mode) Set controller mode to LIVE or SCRIPT.
void	setObjective(int index) Set the objective based on the index (1 to 4).
void	setPlateId(String plateId) Set the plateId, used when no path is specified for the acquire command.
void	setTemperatureRegulation(boolean state) Activate (state=True) or deactivate (state=False) temperature regulation.
void	setTemperatureTarget(double temperature) Set the target temperature in °C, between 18 and 34°C with max 0.1 precision .
void	stopScript() Stop any script currently running.

Methods inherited from class Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TcpIp

public TcpIp()
      throws IOException

Open the TcpIp connection on localhost, and default Port 6200.

Throws:

IOException - if a connection cannot be established (I off, software not running, remote control option not activated)

TcpIp

public TcpIp(int port)
      throws IOException

Open the TcpIp connection to the Imaging Machine (localhost), with custom port.

Throws:

IOException - if a connection cannot be established (I off, software not running, remote control option not activated)

Method Detail

log

public void log(String message)

Log a message to display in the imgui log.

getMode

public TcpIp.ControllerMode getMode()

Return the current controller mode (LIVE/SCRIPT).

getModeAsString

public String getModeAsString()

Return the current controller mode (LIVE/SCRIPT) as a upper-case string.

setMode

public void setMode(String mode)

Alias for setMode(ControllerMode) using "script" or "live" for the mode.

Throws:

IllegalArgumentException - if mode is not one of "script" or "live".

setMode

public void setMode(TcpIp.ControllerMode mode)

Set controller mode to LIVE or SCRIPT.
This command first checks what is the current controller mode to avoid an error.
It also checks that the lid is closed.
Note : Switching to script mode also has the following effects :

• define the timestamp included in the default output directory for the successive acquire commands
• reset the current objective to first objective
• switch-off light sources

openLid

public void openLid()

closeLid

public void closeLid()

isLidOpened

public boolean isLidOpened()

isLidClosed

public boolean isLidClosed()

isLiveMode

public boolean isLiveMode()

Check if currently in live mode.

isScriptMode

public boolean isScriptMode()

Check if currently in script mode.

isTemperatureRegulated

public boolean isTemperatureRegulated()

getTemperatureAmbient

public double getTemperatureAmbient()

Get the current ambient temperature (°C).

getTemperatureSample

public double getTemperatureSample()

Get the current sample temperature (°C).

getTemperatureTarget

public double getTemperatureTarget()

Get the temperature set as target (°C).

setTemperatureTarget

public void setTemperatureTarget(double temperature)

Set the target temperature in °C, between 18 and 34°C with max 0.1 precision .
This does not switch-on temperature regulation, use setTemperatureRegulation(boolean) for this purpose.

setBrightField

public void setBrightField(int channelNumber,
                           int detectionFilter,
                           int intensity,
                           int exposure,
                           boolean lightConstantOn)

Activate the brightfield light lightSource.
In live mode, the resultng "channel" is directly switched on, and must be switched off using the setBrightFieldOff command.
In script mode, the "channel" is switched on with the next acquire commands, synchronously with the camera.

Parameters:

channelNumber - this value is used for the image file name (tag CO).

detectionFilter - positional index of the detection filter (1 to 5), depending on the filter, the overall image intensity varies.

intensity - intensity for the brightfield lightSource (between 0 and 100)

exposure - exposure time in ms, used by the camera when imaging/previewing this channel.
In live mode, a value of 0 will freeze the preview image.

lightConstantOn - if true, the light is constantly on (only during the acquisition in script mode).
if false, the light lightSource is synchronised with the camera exposure, and thus is blinking.

setBrightField

public void setBrightField(int channelNumber,
                           int detectionFilter,
                           int intensity,
                           int exposure)

Same as setBrightField(int, int, int, int, boolean) with default lightConstantOn to false (ie light-source is synchronised with the camera/blinking).

setBrightFieldOff

public void setBrightFieldOff()

Switch-off the brightfield channel if in live-mode, by setting intensity and exposure time to 0.
This also freezes the image preview (exposure=0).
In script mode this has no utility : on/off switching is synchronized with the camera acquisition.
This function thus first check if live mode is active.

setFluoChannel

public void setFluoChannel(int channelNumber,
                           String lightSource,
                           int detectionFilter,
                           int intensity,
                           int exposure,
                           boolean lightConstantOn)

Activate one or multiple LED light sources for fluorescence imaging.
In live mode, the resulting "channel" is directly switched on, and must be switched off using the setFluoChannelOff command.
In script mode, the "channel" is switched on with the next acquire commands, synchronously with the camera.

Parameters:

channelNumber - (>0) this value is used for the image file name (tag CO).

lightSource - this should be a 6-character string of 0 and 1, corresponding to the LED light lightSource to activate.
Ex : "010000" will activate the 2nd light lightSource, while 010001 will activate both the second and last light sources..

detectionFilter - positional index of the detection filter (1 to 5), depending on the filter, the overall image intensity varies.

intensity - intensity for the LED fluorescent light lightSource(s) [0-100]. With multiple light sources, this is the power used for each of them.

exposure - exposure time in ms, used by the camera when imaging/previewing this channel.
In live mode, a value of 0 will freeze the preview image.

lightConstantOn - if true, the light is constantly on (only during the acquisition in script mode).
if false, the light lightSource is synchronised with the camera exposure, and thus is blinking.

setFluoChannel

public void setFluoChannel(int channelNumber,
                           String lightSource,
                           int detectionFilter,
                           int intensity,
                           int exposure)

Same as setFluoChannel(int, String, int, int, int, boolean) with default lightConstantOn to false (ie light-source is synchronised with the camera/blinking).

setFluoChannelOff

public void setFluoChannelOff()

Switch off all the LED light sources (fluorescence) by setting the intensities to 0%.
This also freezes the image preview (exposure=0).
This is effective in live mode only, in script mode on/off switching occurs automatically with the acquire commands.
This function thus first check if live mode is active.

setLightSource

public void setLightSource(int channelNumber,
                           String lightSource,
                           int detectionFilter,
                           int intensity,
                           int exposure,
                           boolean lightConstantOn)

Switch-on light source, brightfield or fluorescent one(s).

Parameters:

channelNumber - (>0) this value is used for the image file name (tag CO).

lightSource - light-source used for the acquisition.
For brightfield, it should be 'brightfield' or 'bf' (not case-sensitive)
For fluorescent light sources, this should be a 6-character string of 0 and 1, corresponding to the LED light lightSource to activate.
Ex : "010000" will activate the 2nd light lightSource, while 010001 will activate both the second and last light sources.

detectionFilter - positional index of the detection filter (1 to 5), depending on the filter, the overall image intensity varies.

intensity - relative intensity for the light-source(s), between 0 and 100.
If multiple fluorescent light sources are activated, this is the intensity used for each of them.

exposure - exposure time in ms

lightConstantOn - if true, the light is constantly on (only during the acquisition in script mode)
if false, the light lightSource is synchronised with the camera exposure, and thus is blinking.

setLightSource

public void setLightSource(int channelNumber,
                           String lightSource,
                           int detectionFilter,
                           int intensity,
                           int exposure)

Same as setLightSource but with default lightConstantOn to false.

setLightSourceOff

public void setLightSourceOff(String lightSource)

Switch-off a light-source (brightfield or fluo).

Parameters:

lightSource - same as in setLightSource(int, String, int, int, int, boolean)

acquireZstack

public String acquireZstack(int channelNumber,
                            int objective,
                            String lightSource,
                            int detectionFilter,
                            int intensity,
                            int exposure,
                            double zStackCenter,
                            int nSlices,
                            double zStepSize,
                            boolean lightConstantOn,
                            String saveDirectory)

Acquire at the current XY-position, a Z-stack composed of nSlices, distributed evenly around a Z-centre position, using current camera settings.
For successive acquire commands (different channels/wells), it is advised to first switch to script mode using setMode(String) to avoid time-consuming switch between script/live mode.

Images are named according to the IM filenaming convention, and saved in saveDirectory, or in the default acquisition directory if none is mentioned. Use setMetadata functions to update image-metadata used for filenaming before calling acquire.

In live mode, this function first switch to script mode (needed for acquire commands) and switch back to live mode after acquisition.

Note : different camera settings can be used between autofocus and acquisition, use setCamera(int, int, int, int, int) before the respective commands.

Parameters:

channelNumber - (>0) this value is used for the image file name (tag CO).

objective - index of the objective to use for acquisition (1 to 4 as in setObjective(int))

lightSource - light-source used for the acquisition.
For brightfield, it should be 'brightfield' or 'bf' (not case-sensitive)
For fluorescent light sources, this should be a 6-character string of 0 and 1, corresponding to the LED light lightSource to activate.
Ex : "010000" will activate the 2nd light lightSource, while 010001 will activate both the second and last light sources.

detectionFilter - positional index of the detection filter (1 to 5). Depending on the filter, the overall image intensity varies.

intensity - relative intensity for the light-source(s), between 0 and 100.
If multiple fluorescent light sources are activated, this is the intensity used for each of them.

exposure - exposure time in ms

zStackCenter - centre position of the Z-stack in µm, with 0.1 precision.
One typically uses the value returned by the autofocus (+/- some offset eventually).

nSlices - Number of slices composing the stack.
For odd number of slices, the centre slice is acquired at Z-position zStackCenter and (nSlices-1)/2 are acquired above and below this center slice.
For even number of slices, nSlices/2 slices are acquired above and below the centre position. No images is acquired for the center position.

zStepSize - distance between slices in µm with 0.1 precision

lightConstantOn - if true, the light is constantly on (only during the acquisition in script mode)
if false, the light lightSource is synchronised with the camera exposure, and thus is blinking.

saveDirectory - Custom directory where the images should be saved. Use double-backslash \\ or single forward slash / as delimiter between path elements.
If null or "", the images are saved within the default project directory, in a subdirectory named with the current acquisition timestamp (defined when switching to script mode) and the default plateID (in the form timestamp_plateID).
Use setDefaultProjectFolder(String) and setPlateId(String) to define the default values for these fields.
The timestamp is generated when the software is switched to script mode, such that for successive acquire commands (for wells and channels) the timestamp is identical, and images end up in the same directory.

Returns:

the path to the directory where the images were saved

See Also:

acquireZstack(int, int, String, int, int, int, double, int, double), acquireVideo(int, int, String, int, int, int, double, int, boolean, String)

acquireZstack

public String acquireZstack(int channelNumber,
                            int objective,
                            String lightSource,
                            int detectionFilter,
                            int intensity,
                            int exposure,
                            double zStackCenter,
                            int nSlices,
                            double zStepSize)

Similar to acquireZstack(int, int, String, int, int, int, double, int, double, boolean, String), but using the default project folder/plateID for the image directory and the light-source blinking (lightConstantOn to false).
For successive acquire commands (different channels/wells), make sure to first switch to script mode using setMode(String) to make sure images from the successive calls to "acquireZstack" are saved in the same directory.

The images are saved within the default project directory, in a subdirectory named with the current acquisition timestamp (defined when switching to script mode) and the default plateID (in the form timestamp_plateID).
Use setDefaultProjectFolder(String) and setPlateId(String) to define the default values for these fields.
The timestamp is generated when the software is switched to script mode, such that for successive acquire commands (for wells and channels) the timestamp is identical, and images end up in the same directory.

acquireVideo

public String acquireVideo(int channelNumber,
                           int objective,
                           String lightSource,
                           int detectionFilter,
                           int intensity,
                           int exposure,
                           double zPosition,
                           int nFrames,
                           boolean lightConstantOn,
                           String saveDirectory)

Acquire a short video of nFrames at the current XY position and given Z-position.
The frame rate will depend on the exposure time, however the exact frame rate cannot be calculated from the exposure, but rather from the image timestamp in the filename.

Parameters:

channelNumber - (>0) this value is used for the image file name (tag CO).

objective - index of the objective to use for acquisition (1 to 4 as in setObjective(int))

lightSource - light-source used for the acquisition.
For brightfield, it should be 'brightfield' or 'bf' (not case-sensitive)
For fluorescent light sources, this should be a 6-character string of 0 and 1, corresponding to the LED light lightSource to activate.
Ex : "010000" will activate the 2nd light lightSource, while 010001 will activate both the second and last light sources.

detectionFilter - positional index of the detection filter (1 to 5). Depending on the filter, the overall image intensity varies.

intensity - relative intensity for the light-source(s), between 0 and 100.
If multiple fluorescent light sources are activated, this is the intensity used for each of them.

exposure - exposure time in ms. This is also the time-interval between frame in the video.

zPosition - Z-axis position of the objective in µm, with 0.1 precision.
One typically uses the value returned by the autofocus (+/- some offset eventually).

nFrames - number of frames in the video.

lightConstantOn - if true, the light is constantly on (only during the acquisition in script mode)
if false, the light lightSource is synchronised with the camera exposure, and thus is blinking.

saveDirectory - Custom directory where the images should be saved. Use double-backslash \\ or single forward slash / as delimiter between path elements.
If null or "", the images are saved within the default project directory, in a subdirectory named with a unique timestamp and the default plateID.
Use setDefaultProjectFolder and setPlateId to define the default values for these fields.

Returns:

the path to the directory where the images were saved

acquireVideo

public String acquireVideo(int channelNumber,
                           int objective,
                           String lightSource,
                           int detectionFilter,
                           int intensity,
                           int exposure,
                           double zPosition,
                           int nFrames)

Same as acquireVideo(int, int, String, int, int, int, double, int, boolean, String) using default project folder for the image directory and lightConstantOn to false.

See Also:

setDefaultProjectFolder(String)

runSoftwareAutoFocus

public double runSoftwareAutoFocus(int objective,
                                   String lightSource,
                                   int detectionFilter,
                                   int intensity,
                                   int exposure,
                                   double zStackCenter,
                                   int nSlices,
                                   double zStepSize,
                                   boolean lightConstantOn)

Run a software autofocus with a custom channel and current objective and camera settings.
Return the Z-position of the most focused slice, within a stack centred on a given Z-position, with nSlices each separated by zStepSize.
This function works with both 'live' and 'script' modes.
NOTE : Different camera settings can be used between the autofocus and the acquisition, use setCamera before each command respectively.

Parameters:

lightSource - light-source used for the acquisition.
For brightfield, it should be 'brightfield' or 'bf' (not case-sensitive)
For fluorescent light sources, this should be a 6-character string of 0 and 1, corresponding to the LED light lightSource to activate.
Ex : "010000" will activate the 2nd light lightSource, while 010001 will activate both the second and last light sources.

detectionFilter - positional index of the detection filter (1 to 5).
Depending on the filter, the overall image intensity varies.

intensity - relative intensity for the light-source(s), between 0 and 100.
If multiple fluorescent light sources are activated, this is the intensity used for each of them.

exposure - exposure time in ms

zStackCenter - centre position of the Z-stack in µm, with 0.1 precision.
One typically uses the value returned by the autofocus (+/- some offset eventually).

nSlices - Number of slices composing the stack.
For odd number of slices, the center slice is acquired at Z-position zStackCenter and (nSlices-1)/2 are acquired above and below this center slice.
For even number of slices, nSlices/2 slices are acquired above and below the center position. No images is acquired for the center position.

zStepSize - distance between slices in µm with 0.1 precision

lightConstantOn - if true, the light is constantly on (only during the acquisition in script mode).
if false, the light lightSource is synchronized with the camera exposure, and thus is blinking.

Returns:

the position of the most focused slice in µm

runSoftwareAutoFocus

public double runSoftwareAutoFocus(int objective,
                                   String lightSource,
                                   int detectionFilter,
                                   int intensity,
                                   int exposure,
                                   double zStackCenter,
                                   int nSlices,
                                   double zStepSize)

Same as runSoftwareAutoFocus(int, String, int, int, int, double, int, double, boolean) with lightConstantOn default to false.
Meaning the light source is synchronised with the camera exposure ie it is blinking.

runHardwareAutoFocus

public double runHardwareAutoFocus(int objective,
                                   int detectionFilter,
                                   double zStart,
                                   double calibrationOffset)

Run a hardware autofocus and return the Z-position found.
The hardware autofocus uses a dedicated laser for focusing.

Parameters:

objective - Objective index used for autofocus, one of 1,2,3,4.
The indexes are almost always ordered by increasing objective magnification.

detectionFilter - Positional index of the detection filter used for the autofocus.

zStart - Starting position for the autofocus search.

calibrationOffset - this value should be read from IM Control Software, tab autofocus when clicking "calibration" for hardware autofocus.

Returns:

The Z-position found by the autofocus.

setTemperatureRegulation

public void setTemperatureRegulation(boolean state)

Activate (state=True) or deactivate (state=False) temperature regulation.
The temperature regulation aims at adjusting the sample temperature to the target temperature.

getNumberOfColumns

public int getNumberOfColumns()

Return the number of plate columns.

getNumberOfRows

public int getNumberOfRows()

Return the number of plate rows.

getObjectiveIndex

public int getObjectiveIndex()

Return the currently selected objective-index (1 to 4).
Typically the objective index are as follow 1:2x, 2:4x, 3:10x, 4:20x, but this might change for custom IM configurations.

setObjective

public void setObjective(int index)

Set the objective based on the index (1 to 4).
Typically the objective index are as follow 1:2x, 2:4x, 3:10x, 4:20x, but this might change for custom IM configurations.
If the selected objective is already the current objective, the command has no effect.

setDefaultProjectFolder

public void setDefaultProjectFolder(String folder)

Set the default project folder, used when no path is specified for the acquire command.
Use double-backslash \\ or single forward slash / as delimiter between path elements.
Images will be saved in subfolders of this default project folder, in unique subfolders named with a timestamp, followed by the PlateId, i.e DefaultProjectFolder > timestamp_PlateId.

See Also:

setPlateId(String)

setPlateId

public void setPlateId(String plateId)

Set the plateId, used when no path is specified for the acquire command.
Images will be saved in subfolders of the default project folder, in unique subfolders named with a timestamp, followed by the PlateId, i.e DefaultProjectFolder > timestamp_PlateId.

See Also:

setDefaultProjectFolder(String)

setMetadata

public void setMetadata(String wellId,
                        int wellNumber,
                        int subposition,
                        int timepoint)

Update multiple metadata at once, used to name image files for the next acquisition(s).

setMetadataWellNumber

public void setMetadataWellNumber(int number)

setMetadataWellId

public void setMetadataWellId(String wellID,
                              char leadingChar)

Update the well ID (ex: "A001"), used to name the image files for the next acquisitions. The well ID must start with a letter.

Parameters:

wellID -

leadingChar - Character added before the well id, at the beginning of the filename.

setMetadataWellId

public void setMetadataWellId(String wellID)

Update the well ID (ex: "A001") using the default leading character '-' for compatibility with Acquifer software suite.

setMetadataSubposition

public void setMetadataSubposition(int subposition)

Update the well subposition index (within a given well), used to name the image files for the next acquisitions (PO tag).

setMetadataTimepoint

public void setMetadataTimepoint(int timepoint)

Update the timepoint (or loop iteration) index, used to name the image files for the next acquisitions (LO tag).

setMetadataChannel

public void setMetadataChannel(int channel)

Update the channel metadata used to name the image files for the next acquisitions (CO tag).
This tag is overwritten by the value given in acquire command.

getPositionX

public double getPositionX()

Return the current objective x-axis position in mm.

getPositionY

public double getPositionY()

Return the current objective y-axis position in mm.

getPositionZ

public double getPositionZ()

Return the current objective z-axis position in µm.

moveXYto

public void moveXYto(double x,
                     double y)

Move x,y to target position (mode Absolute), in mm with 0.001 decimal precision.

moveXYto

public void moveXYto(acquifer.core.WellPosition wellPosition)

Move x,y to a specific well position and update current well/subposition metadata.

moveXYby

public void moveXYby(double x,
                     double y)

Move x,y by a given step-size (mode Relative), in mm with 0.001 decimal precision.

moveZto

public void moveZto(double z)

Move Z-position to target position (mode Absolute), in µm with 0.1 precision.

moveZby

public void moveZby(double z)

Move Z-position by given step size (mode Relative), in µm with 0.1 precision.

moveXYZto

public void moveXYZto(double x,
                      double y,
                      double z)

Move to x,y position (mm, 0.001 precision) and z-position in µm (0.1 precision).

runScript

public void runScript(String scriptPath)

Start a .imsf or .cs script to run an acquisition.
This command can be called only if no script is running.

setCamera

public void setCamera(int x,
                      int y,
                      int width,
                      int height,
                      int binning)

Set camera acquisition settings such as sensor area used for acquisition and binning factor.
The full camera sensor area corresponds to a 2048 x 2048 square of non-binned pixels.
The settings will apply to the next "Acquire" commands, issued via the GUI or via TCPIP.

Parameters:

x - coordinate of the top-left pixel for the sensor area (in non-binned pixel units).

y - coordinate of the top-left pixel for the sensor area (in non-binned pixel units).

width - of the camera sensor area in pixel (in non-binned pixel units).

height - of the camera sensor area in pixel (in non-binned pixel units).

binning - one of 1 (no binning), 2 (2x2), 4 (4x4)

setCamera

public void setCamera(int x,
                      int y,
                      int width,
                      int height)

Set the fraction of the camera sensor used for the next acquisition, also reset binning to default (1=no binning).
This is like calling setCamera(x,y,width,height,1).
Full camera frame corresponds to a 2048x2048 rectangle of un-binned pixels.
To set both a custom sensor region and binning factor, use setCamera(int, int, int, int, int).

setCameraBinning

public void setCameraBinning(int binning)

Set the binning factor (1,2 or 4), also reset the camera sensor area to full-frame (2048x2048).

resetCamera

public void resetCamera()

Reset camera to full-size field of view (2048x2048 pixels) and no binning.

stopScript

public void stopScript()

Stop any script currently running.
This cannot be called with the same IM object after calling runScript.
Create a new IM object to establish a parallel connection and stop the script.

convertXYpixelToMillimeters

public static double[] convertXYpixelToMillimeters(int x,
                                                   int y,
                                                   String imageName,
                                                   int width,
                                                   int height)

Convert from pixel coordinates in an image to the corresponding objective axis-coordinates of the imaging machine.
The image must be acquired with the full camera sensor area, so that the centre of the image, corresponds to the objective axis-coordinates in the image filename.
This assumption is not true when a region of interest was used as sensor area, that was not centred in the original field of view.
Pixel coordinates are considered to have the 0 in the centre of the pixel (as in ImageJ), ie a pixel extend from coordinates -0.5 to 0.5.
This works for IM04 only (for extraction of metadata from filename).

Parameters:

x - pixel coordinate in the image, to convert to objective X-axis position

y - pixel coordinate in the image, to convert to objective Y-axis position

imageName - used to recover the XY axis-position of the objective (in mm) and the pixel-size.

width - image width in pixels, used to recalculate the image centere (same for height)

height - image height in pixels

closeConnection

public void closeConnection()

Close the tcpip connection, no more commands can be sent to the IM with this object after that.
The command also switch back to live mode (if not already the case) and switch off any light source that could be on.