A B C D E F G H I K L M N O P R S T U V W X Y Z 

A

acquisitionExists(String) - Method in interface org.micromanager.api.ScriptInterface
Checks whether an acquisition with the given name already exists.
add(StagePosition) - Method in class org.micromanager.api.MultiStagePosition
Add one stage position point
addChangeListener(ChangeListener) - Method in class org.micromanager.api.PositionList
 
addImageCacheListener(ImageCacheListener) - Method in interface org.micromanager.api.ImageCache
Adds the provided cache listener.
addImageProcessor(DataProcessor<TaggedImage>) - Method in interface org.micromanager.api.ScriptInterface
Adds an image processor to the DataProcessor pipeline.
addImageToAcquisition(String, int, int, int, int, TaggedImage) - Method in interface org.micromanager.api.ScriptInterface
Inserts image into the data set.
addMMBackgroundListener(Component) - Method in interface org.micromanager.api.ScriptInterface
Lets Components register themselves so that their background can be manipulated by the Micro-Manager UI.
addMMListener(MMListenerInterface) - Method in interface org.micromanager.api.ScriptInterface
Allows MMListeners to register themselves so that they will receive alerts as defined in the MMListenerInterface
addPosition(MultiStagePosition) - Method in class org.micromanager.api.PositionList
Adds a new position to the list.
addPosition(int, MultiStagePosition) - Method in class org.micromanager.api.PositionList
Insert a position into the list.
addToAlbum(TaggedImage) - Method in interface org.micromanager.api.ScriptInterface
Add a TaggedImage to an album; creates a new album if the image and current album do not match in image dimensions, bits per pixel, bytes per pixel, or number of channels.
AF_KEY - Static variable in class org.micromanager.api.PositionList
 
AF_VALUE_FULL - Static variable in class org.micromanager.api.PositionList
 
AF_VALUE_INCREMENTAL - Static variable in class org.micromanager.api.PositionList
 
AF_VALUE_NONE - Static variable in class org.micromanager.api.PositionList
 
applySettings() - Method in interface org.micromanager.api.Autofocus
 
attachRunnable(int, int, int, int, Runnable) - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
attachRunnable(int, int, int, int, Runnable) - Method in interface org.micromanager.api.ScriptInterface
Attach a runnable to the acquisition engine.
Autofocus - Interface in org.micromanager.api
 
autostretchCurrentWindow() - Method in interface org.micromanager.api.ScriptInterface
Autostretch each histogram for the currently-active window, as if the "Auto" button had been clicked for each one.

B

BIT_DEPTH - Static variable in class org.micromanager.api.MMTags.Image
 
BIT_DEPTH - Static variable in class org.micromanager.api.MMTags.Summary
 

C

cameraTimeout - Variable in class org.micromanager.api.SequenceSettings
 
CHANNEL - Static variable in class org.micromanager.api.MMTags.Image
 
CHANNEL_DEFAULT - Static variable in class org.micromanager.api.MMTags.Values
 
CHANNEL_INDEX - Static variable in class org.micromanager.api.MMTags.Image
 
CHANNEL_MAXES - Static variable in class org.micromanager.api.MMTags.Summary
 
CHANNEL_MINS - Static variable in class org.micromanager.api.MMTags.Summary
 
CHANNEL_NAME - Static variable in class org.micromanager.api.MMTags.Image
 
channelGroup - Variable in class org.micromanager.api.SequenceSettings
 
CHANNELS - Static variable in class org.micromanager.api.MMTags.Summary
 
channels - Variable in class org.micromanager.api.SequenceSettings
 
clearAllPositions() - Method in class org.micromanager.api.PositionList
Empties the list.
clearMessageWindow() - Method in interface org.micromanager.api.ScriptInterface
Clears scripting console output window.
clearRunnables() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
clearRunnables() - Method in interface org.micromanager.api.ScriptInterface
Remove runnables from the acquisition engine
close() - Method in interface org.micromanager.api.TaggedImageStorage
Disposes of the tagged images from memory -- images will only be stored in disk.
closeAcquisition(String) - Method in interface org.micromanager.api.ScriptInterface
Closes the acquisition.
closeAcquisitionWindow(String) - Method in interface org.micromanager.api.ScriptInterface
Closes the image window corresponding to the acquisition.
closeAllAcquisitions() - Method in interface org.micromanager.api.ScriptInterface
Closes all currently open acquisitions.
COLORS - Static variable in class org.micromanager.api.MMTags.Summary
 
comment - Variable in class org.micromanager.api.SequenceSettings
 
computeScore(ImageProcessor) - Method in interface org.micromanager.api.Autofocus
Computes a focus score for the given image
configGroupChangedAlert(String, String) - Method in interface org.micromanager.api.MMListenerInterface
 
ConfigGroupChangedEvent - Class in org.micromanager.api.events
 
ConfigGroupChangedEvent(String, String) - Constructor for class org.micromanager.api.events.ConfigGroupChangedEvent
 
createAcquisition(JSONObject, boolean, boolean) - Method in interface org.micromanager.api.ScriptInterface
Deprecated.
Use openAcquisition() instead.
customIntervalsMs - Variable in class org.micromanager.api.SequenceSettings
 

D

DataProcessor<E> - Class in org.micromanager.api
A DataProcessor thread allows for on-the-fly modification of image data during acquisition.
DataProcessor() - Constructor for class org.micromanager.api.DataProcessor
 
DIRECTORY - Static variable in class org.micromanager.api.MMTags.Summary
 
displayImage(TaggedImage) - Method in interface org.micromanager.api.ScriptInterface
Show a TaggedImage in the snap/live window (uses current camera settings to figure out the shape of the image)
dispose() - Method in class org.micromanager.api.DataProcessor
Remove all GUI elements generated by makeConfigurationGUI().
dispose() - Method in interface org.micromanager.api.MMPlugin
The main app calls this method to remove the module window

E

ELAPSED_TIME - Static variable in class org.micromanager.api.MMTags.Summary
 
ELAPSED_TIME_MS - Static variable in class org.micromanager.api.MMTags.Image
 
enableContinuousFocus(boolean) - Method in interface org.micromanager.api.Autofocus
 
enableLiveMode(boolean) - Method in interface org.micromanager.api.ScriptInterface
Turn live mode on or off (equivalent to pressing the Live mode button).
enableRoiButtons(boolean) - Method in interface org.micromanager.api.ScriptInterface
Enabled or disable the ROI buttons on the main window.
exposureChanged(String, double) - Method in interface org.micromanager.api.MMListenerInterface
Implement to be notified that the exposure time given camera has changed
ExposureChangedEvent - Class in org.micromanager.api.events
 
ExposureChangedEvent(String, double) - Constructor for class org.micromanager.api.events.ExposureChangedEvent
 

F

finished() - Method in interface org.micromanager.api.TaggedImageStorage
Call this function when no more images are expected Finishes writing the metadata file and closes it.
focus(double, int, double, int) - Method in interface org.micromanager.api.Autofocus
OBSOLETE - do not use this method.
FRAME - Static variable in class org.micromanager.api.MMTags.Image
 
FRAME_INDEX - Static variable in class org.micromanager.api.MMTags.Image
 
FRAMES - Static variable in class org.micromanager.api.MMTags.Summary
 
fromJSONStream(String) - Static method in class org.micromanager.api.SequenceSettings
 
fullFocus() - Method in interface org.micromanager.api.Autofocus
 

G

generateLabel() - Method in class org.micromanager.api.PositionList
Helper method to generate unique label when inserting a new position.
generateLabel(String) - Method in class org.micromanager.api.PositionList
 
get(int) - Method in class org.micromanager.api.MultiStagePosition
Return stage position based on index
get(String) - Method in class org.micromanager.api.MultiStagePosition
Returns position for a specific stage.
getAcqDlg() - Method in interface org.micromanager.api.ScriptInterface
Deprecated.
Use the get/setAcquisitionSettings() interface instead.
getAcquisition(String) - Method in interface org.micromanager.api.ScriptInterface
Deprecated.
Because it returns an internal object that is subject to change.
getAcquisitionEngine2010() - Method in interface org.micromanager.api.ScriptInterface
 
getAcquisitionImageBitDepth(String) - Method in interface org.micromanager.api.ScriptInterface
Returns the number of bits used per pixel
getAcquisitionImageByteDepth(String) - Method in interface org.micromanager.api.ScriptInterface
Returns the number of bytes used per pixel
getAcquisitionImageCache(String) - Method in interface org.micromanager.api.ScriptInterface
Get a reference to the ImageCache object associated with the acquisition.
getAcquisitionImageHeight(String) - Method in interface org.micromanager.api.ScriptInterface
Returns the width (in pixels) of images in this acquisition
getAcquisitionImageWidth(String) - Method in interface org.micromanager.api.ScriptInterface
Returns the width (in pixels) of images in this acquisition
getAcquisitionMultiCamNumChannels(String) - Method in interface org.micromanager.api.ScriptInterface
Returns boolean specifying whether multiple cameras used in this acquisition
getAcquisitionNames() - Method in interface org.micromanager.api.ScriptInterface
Gets an Array with names of all open acquisitions
getAcquisitionPath() - Method in interface org.micromanager.api.ScriptInterface
Return the current acquisition path, or null if not applicable
getAcquisitionSettings() - Method in interface org.micromanager.api.ScriptInterface
Return current acquisition settings
getAutofocus() - Method in interface org.micromanager.api.ScriptInterface
Currently active autofocus device (can be either a Java or C++ coded device).
getAutofocusManager() - Method in interface org.micromanager.api.ScriptInterface
 
getBackgroundColor() - Method in interface org.micromanager.api.ScriptInterface
Returns the current color of the main window so that it can be used in derived windows/plugins as well
getBackgroundStyle() - Method in interface org.micromanager.api.ScriptInterface
 
getBitDepth() - Method in interface org.micromanager.api.ImageCache
Returns the bit depth of all images in the image cache.
getCacheForWindow(ImageWindow) - Method in interface org.micromanager.api.ScriptInterface
Given an ImageWindow, return the ImageCache associated with it.
getCameraName() - Method in class org.micromanager.api.events.ExposureChangedEvent
 
getChangingKeys() - Method in interface org.micromanager.api.ImageCache
Get a list of keys that are not identical for every TaggedImage.
getChannelColor(int) - Method in interface org.micromanager.api.ImageCache
Returns the preferred display color for a channel, specified by channelIndex.
getChannelExposureTime(String, String, double) - Method in interface org.micromanager.api.ScriptInterface
Returns exposure time for the desired preset in the given channelgroup Acquires its info from the preferences Same thing is used in MDA window, but this class keeps its own copy
getChannelGamma(int) - Method in interface org.micromanager.api.ImageCache
Returns the gamma for the channel display.
getChannelHistogramMax(int) - Method in interface org.micromanager.api.ImageCache
Returns the preferred maximum value for the channel's histogram.
getChannelMax(int) - Method in interface org.micromanager.api.ImageCache
Gets the maximum intensity value for a channel display (typically shown as full intensity color).
getChannelMin(int) - Method in interface org.micromanager.api.ImageCache
Gets the minimum intensity value for a channel display (typically shown as black).
getChannelName(int) - Method in interface org.micromanager.api.ImageCache
Returns the name of a channel specified by channelIndex.
getChannelSetting(int) - Method in interface org.micromanager.api.ImageCache
Returns a JSONObject with channel settings for the channel whose index is the argument.
getComment() - Method in interface org.micromanager.api.ImageCache
Gets the overall comment string for this data set.
getCopyright() - Method in interface org.micromanager.api.MMBasePlugin
Returns copyright information
getCurrentAlbum() - Method in interface org.micromanager.api.ScriptInterface
Returns the name of the current album (i.e.
getCurrentFocusScore() - Method in interface org.micromanager.api.Autofocus
 
getDataSetSize() - Method in interface org.micromanager.api.TaggedImageStorage
 
getDefaultXYStage() - Method in class org.micromanager.api.MultiStagePosition
 
getDefaultZStage() - Method in class org.micromanager.api.MultiStagePosition
 
getDescription() - Method in interface org.micromanager.api.MMBasePlugin
Returns a very short (few words) description of the module.
getDevice() - Method in class org.micromanager.api.events.PropertyChangedEvent
 
getDeviceName() - Method in interface org.micromanager.api.Autofocus
 
getDeviceName() - Method in class org.micromanager.api.events.SLMExposureChangedEvent
 
getDeviceName() - Method in class org.micromanager.api.events.StagePositionChangedEvent
 
getDeviceName() - Method in class org.micromanager.api.events.XYStagePositionChangedEvent
 
getDiskLocation() - Method in interface org.micromanager.api.TaggedImageStorage
 
getDisplayAndComments() - Method in interface org.micromanager.api.TaggedImageStorage
 
getDisplayMode() - Method in interface org.micromanager.api.ImageCache
Returns the display mode used by the CompositeImage (composite, color, or grayscale)
getGridColumn() - Method in class org.micromanager.api.MultiStagePosition
Returns rectangular grid column.
getGridRow() - Method in class org.micromanager.api.MultiStagePosition
Returns rectangular grid row.
getGroupName() - Method in class org.micromanager.api.events.ConfigGroupChangedEvent
 
getHideMDADisplayOption() - Method in interface org.micromanager.api.ScriptInterface
 
getImage(int, int, int, int) - Method in interface org.micromanager.api.ImageCache
Return the TaggedImage at the specified coordinates, or null if that image does not exist.
getImage(int, int, int, int) - Method in interface org.micromanager.api.TaggedImageStorage
 
getImageCacheListeners() - Method in interface org.micromanager.api.ImageCache
Gets a list of image cache listeners.
getImageComment(JSONObject) - Method in interface org.micromanager.api.ImageCache
Returns the image comment for a particular image.
getImageMetadata(int, int, int, int) - Method in class org.micromanager.api.MMWindow
Note: this function is preliminary.
getImagePlus(int) - Method in class org.micromanager.api.MMWindow
Returns an ImageJ ImagePlus for a given position Does not update the display
getImageProcessor(int, int, int, int) - Method in class org.micromanager.api.MMWindow
 
getImageProcessorPipeline() - Method in interface org.micromanager.api.ScriptInterface
Retrieve a copy of the current DataProcessor pipeline.
getImageTags(int, int, int, int) - Method in interface org.micromanager.api.TaggedImageStorage
 
getInfo() - Method in interface org.micromanager.api.MMBasePlugin
Returns verbose information about the module.
getIsEnabled() - Method in class org.micromanager.api.DataProcessor
Get whether or not this Processor is enabled.
getIsOpen() - Method in interface org.micromanager.api.ImageCache
Return true if the ImageCache is still valid, false otherwise.
getLabel() - Method in class org.micromanager.api.MultiStagePosition
Returns position label.
getLastImageTags() - Method in interface org.micromanager.api.ImageCache
Returns the image tags for the last received image.
getMMCore() - Method in interface org.micromanager.api.ScriptInterface
Provides access to the Core and its functionality.
getNewConfig() - Method in class org.micromanager.api.events.ConfigGroupChangedEvent
 
getNewExposureTime() - Method in class org.micromanager.api.events.ExposureChangedEvent
 
getNewExposureTime() - Method in class org.micromanager.api.events.SLMExposureChangedEvent
 
getNewPixelSizeUm() - Method in class org.micromanager.api.events.PixelSizeChangedEvent
 
getNumberOfChannels() - Method in class org.micromanager.api.MMWindow
 
getNumberOfFrames() - Method in class org.micromanager.api.MMWindow
 
getNumberOfImages() - Method in interface org.micromanager.api.Autofocus
 
getNumberOfPositions() - Method in class org.micromanager.api.MMWindow
 
getNumberOfPositions() - Method in class org.micromanager.api.PositionList
Returns the number of positions contained within the list
getNumberOfSlices() - Method in class org.micromanager.api.MMWindow
 
getNumDisplayChannels() - Method in interface org.micromanager.api.ImageCache
Returns the number of channels in the ImageCache.
getPixelType() - Method in interface org.micromanager.api.ImageCache
Returns the pixel type for images in this image cache.
getPos() - Method in class org.micromanager.api.events.StagePositionChangedEvent
 
getPosition() - Method in class org.micromanager.api.MMWindow
Returns the current position of the image viewer Positions are 1-based
getPosition(int) - Method in class org.micromanager.api.PositionList
Returns multi-stage position associated with the position index.
getPositionCopy(int) - Method in class org.micromanager.api.PositionList
Returns a copy of the multi-stage position associated with the position index.
getPositionIndex(String) - Method in class org.micromanager.api.PositionList
Returns position index associated with the position name.
getPositionList() - Method in interface org.micromanager.api.ScriptInterface
Returns a copy of the current PositionList, the one used by the Acquisition Protocol
getPositions() - Method in class org.micromanager.api.PositionList
Returns an array of positions contained in the list.
getProperties() - Method in interface org.micromanager.api.Autofocus
 
getProperty(String) - Method in interface org.micromanager.api.Autofocus
 
getProperty() - Method in class org.micromanager.api.events.PropertyChangedEvent
 
getProperty(String) - Method in class org.micromanager.api.MultiStagePosition
Returns property value for a given key (name)
getPropertyNames() - Method in interface org.micromanager.api.Autofocus
 
getPropertyNames() - Method in class org.micromanager.api.MultiStagePosition
Return the array of property keys (names) associated with this position
getPropertyValue(String) - Method in interface org.micromanager.api.Autofocus
 
getROI() - Method in interface org.micromanager.api.ScriptInterface
Get the default camera's ROI -- a convenience function.
getSnapLiveWin() - Method in interface org.micromanager.api.ScriptInterface
Returns the ImageJ ImageWindow instance that is used for Snap and Live display.
getSummaryMetadata() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
getSummaryMetaData() - Method in class org.micromanager.api.MMWindow
Note: this function is preliminary.
getSummaryMetadata() - Method in interface org.micromanager.api.TaggedImageStorage
 
getTaggedImage(int, int, int, int) - Method in class org.micromanager.api.MMWindow
 
getUniqueAcquisitionName(String) - Method in interface org.micromanager.api.ScriptInterface
Returns a name beginning with stem that is not yet used.
getValue() - Method in class org.micromanager.api.events.PropertyChangedEvent
 
getVerbose() - Method in class org.micromanager.api.StagePosition
 
getVerboseStatus() - Method in interface org.micromanager.api.Autofocus
 
getVersion() - Method in interface org.micromanager.api.MMBasePlugin
Returns version string for the module.
getVersion() - Method in interface org.micromanager.api.ScriptInterface
 
getX() - Method in class org.micromanager.api.MultiStagePosition
Returns "X" coordinate of the position.
getXPos() - Method in class org.micromanager.api.events.XYStagePositionChangedEvent
 
getXYPosListDlg() - Method in interface org.micromanager.api.ScriptInterface
Deprecated.
Use the get/setPositionList() interface instead.
getXYStageName() - Method in interface org.micromanager.api.ScriptInterface
There can be multiple XY stage devices in a system.
getXYStagePosition() - Method in interface org.micromanager.api.ScriptInterface
Obtain the current XY stage position.
getY() - Method in class org.micromanager.api.MultiStagePosition
Returns "Y" coordinate of the position.
getYPos() - Method in class org.micromanager.api.events.XYStagePositionChangedEvent
 
getZ() - Method in class org.micromanager.api.MultiStagePosition
Returns "Z" - focus coordinate of the position.
goToPosition(MultiStagePosition, CMMCore) - Static method in class org.micromanager.api.MultiStagePosition
Moves all stages to the specified positions.

H

hasProperty(String) - Method in class org.micromanager.api.MultiStagePosition
Checks if the position has a particular property
HEIGHT - Static variable in class org.micromanager.api.MMTags.Image
 
HEIGHT - Static variable in class org.micromanager.api.MMTags.Summary
 

I

IAcquisitionEngine2010 - Interface in org.micromanager.api
This interface is implemented by AcquisitionEngine2010 (generated by the clojure code in micromanager/acqEngine).
IJ_TYPE - Static variable in class org.micromanager.api.MMTags.Image
 
IJ_TYPE - Static variable in class org.micromanager.api.MMTags.Summary
 
ImageCache - Interface in org.micromanager.api
An interface, implemented by MMImageCache.
ImageCacheListener - Interface in org.micromanager.api
This interface provides a way to register callbacks to monitor the state of an ImageCache.
imageKeys() - Method in interface org.micromanager.api.TaggedImageStorage
 
imageReceived(TaggedImage) - Method in interface org.micromanager.api.ImageCacheListener
 
imagingFinished(String) - Method in interface org.micromanager.api.ImageCacheListener
 
incrementalFocus() - Method in interface org.micromanager.api.Autofocus
 
initializeAcquisition(String, int, int, int, int) - Method in interface org.micromanager.api.ScriptInterface
Set up image physical dimensions for the data set that has already been opened.
installAutofocusPlugin(String) - Method in interface org.micromanager.api.ScriptInterface
Installs an autofocus plugin class from the class path.
intervalMs - Variable in class org.micromanager.api.SequenceSettings
 
isAcquisitionRunning() - Method in interface org.micromanager.api.ScriptInterface
Returns true when an acquisition is currently running (note: this function will not return true if live mode, snap, or "Camera --> Album" is currently running
isContinuousFocusEnabled() - Method in interface org.micromanager.api.Autofocus
 
isContinuousFocusLocked() - Method in interface org.micromanager.api.Autofocus
 
isFinished() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
isFinished() - Method in interface org.micromanager.api.TaggedImageStorage
 
isLabelUnique(String) - Method in class org.micromanager.api.PositionList
Verify that the new label is unique
isLiveModeOn() - Method in interface org.micromanager.api.ScriptInterface
Determines whether live mode is currently running.
isMMWindow() - Method in class org.micromanager.api.MMWindow
 
isPaused() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
isPaused() - Method in interface org.micromanager.api.ScriptInterface
Returns true if the acquisition is currently paused.
isRunning() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
isStarted() - Method in class org.micromanager.api.DataProcessor
Returns true if the DataProcessor has started up and objects are being processed as they arrive.

K

keepShutterOpenChannels - Variable in class org.micromanager.api.SequenceSettings
 
keepShutterOpenSlices - Variable in class org.micromanager.api.SequenceSettings
 

L

lastAcquiredFrame() - Method in interface org.micromanager.api.TaggedImageStorage
 
load(String) - Method in class org.micromanager.api.PositionList
Load position list from a file.
loadAcquisition(String) - Method in interface org.micromanager.api.ScriptInterface
Loads setting for Acquisition Dialog from file Will open Acquisition Dialog when it is not open yet
logError(Exception, String) - Method in interface org.micromanager.api.ScriptInterface
Writes the stacktrace and a message to the Micro-Manager log (Corelog.txt).
logError(Exception) - Method in interface org.micromanager.api.ScriptInterface
Writes a stacktrace to the Micro-Manager log.
logError(String) - Method in interface org.micromanager.api.ScriptInterface
Writes an error to the Micro-Manager log (same as logMessage).
logMessage(String) - Method in interface org.micromanager.api.ScriptInterface
Adds a message to the Micro-Manager log (found in Corelogtxt).
logStartupProperties() - Method in interface org.micromanager.api.ScriptInterface
Write various properties of MM and the OS to the log.

M

main(String[]) - Static method in class org.micromanager.api.SequenceSettings
 
makeActive() - Method in interface org.micromanager.api.ScriptInterface
 
makeConfigurationGUI() - Method in class org.micromanager.api.DataProcessor
Generate and show the GUI needed to configure the DataProcessor.
markCurrentPosition() - Method in interface org.micromanager.api.ScriptInterface
Opens the XYPositionList when it is not opened.
message(String) - Method in interface org.micromanager.api.ScriptInterface
Displays text in the scripting console output window.
MMBasePlugin - Interface in org.micromanager.api
In practice no user code should directly implement this interface; instead they should implement MMPlugin or MMProcessorPlugin.
MMListenerInterface - Interface in org.micromanager.api
 
MMPlugin - Interface in org.micromanager.api
Implement this interface to create Micro-Manager plugins.
MMProcessorPlugin - Interface in org.micromanager.api
Implement this interface to create Micro-Manager DataProcessor plugins.
MMTags - Class in org.micromanager.api
The list of tags used by the Micro-manager
MMTags() - Constructor for class org.micromanager.api.MMTags
 
MMTags.Image - Class in org.micromanager.api
 
MMTags.Image() - Constructor for class org.micromanager.api.MMTags.Image
 
MMTags.Root - Class in org.micromanager.api
Meta-tags referring to main sections of the metadata
MMTags.Root() - Constructor for class org.micromanager.api.MMTags.Root
 
MMTags.Summary - Class in org.micromanager.api
Summary tags
MMTags.Summary() - Constructor for class org.micromanager.api.MMTags.Summary
 
MMTags.Values - Class in org.micromanager.api
 
MMTags.Values() - Constructor for class org.micromanager.api.MMTags.Values
 
MMWindow - Class in org.micromanager.api
 
MMWindow(ImagePlus) - Constructor for class org.micromanager.api.MMWindow
 
MultiStagePosition - Class in org.micromanager.api
 
MultiStagePosition() - Constructor for class org.micromanager.api.MultiStagePosition
Default constructor.
MultiStagePosition(String, double, double, String, double) - Constructor for class org.micromanager.api.MultiStagePosition
Convenient constructor where the motion system consists of one XY stage and one focus stage.

N

NAMES - Static variable in class org.micromanager.api.MMTags.Summary
 
newInstance(MultiStagePosition) - Static method in class org.micromanager.api.MultiStagePosition
Copy constructor.
newInstance(PositionList) - Static method in class org.micromanager.api.PositionList
 
newInstance(StagePosition) - Static method in class org.micromanager.api.StagePosition
 
nextWakeTime() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
notifyChangeListeners() - Method in class org.micromanager.api.PositionList
 
numAxes - Variable in class org.micromanager.api.StagePosition
 
numFrames - Variable in class org.micromanager.api.SequenceSettings
 

O

OBJECTIVE_LABEL - Static variable in class org.micromanager.api.MMTags.Summary
 
openAcquisition(String, String, int, int, int, int, boolean, boolean) - Method in interface org.micromanager.api.ScriptInterface
Opens a new acquisition data set
openAcquisitionData(String, boolean) - Method in interface org.micromanager.api.ScriptInterface
Open an existing data set.
openAcquisitionData(String, boolean, boolean) - Method in interface org.micromanager.api.ScriptInterface
Open an existing data set.
org.micromanager.api - package org.micromanager.api
 
org.micromanager.api.events - package org.micromanager.api.events
 

P

pause() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
PIX_TYPE - Static variable in class org.micromanager.api.MMTags.Image
 
PIX_TYPE - Static variable in class org.micromanager.api.MMTags.Summary
 
PIX_TYPE_GRAY_16 - Static variable in class org.micromanager.api.MMTags.Values
 
PIX_TYPE_GRAY_8 - Static variable in class org.micromanager.api.MMTags.Values
 
PIX_TYPE_RGB_32 - Static variable in class org.micromanager.api.MMTags.Values
 
PIX_TYPE_RGB_64 - Static variable in class org.micromanager.api.MMTags.Values
 
PIXEL_ASPECT - Static variable in class org.micromanager.api.MMTags.Summary
 
pixelSizeChangedAlert(double) - Method in interface org.micromanager.api.MMListenerInterface
 
PixelSizeChangedEvent - Class in org.micromanager.api.events
 
PixelSizeChangedEvent(double) - Constructor for class org.micromanager.api.events.PixelSizeChangedEvent
 
PIXSIZE - Static variable in class org.micromanager.api.MMTags.Summary
 
POS_INDEX - Static variable in class org.micromanager.api.MMTags.Image
 
POS_NAME - Static variable in class org.micromanager.api.MMTags.Image
 
PositionList - Class in org.micromanager.api
Navigation list of positions for the XYStage.
PositionList() - Constructor for class org.micromanager.api.PositionList
 
POSITIONS - Static variable in class org.micromanager.api.MMTags.Summary
 
PREFIX - Static variable in class org.micromanager.api.MMTags.Summary
 
prefix - Variable in class org.micromanager.api.SequenceSettings
 
promptToSaveAcquisition(String, boolean) - Method in interface org.micromanager.api.ScriptInterface
Display dialog to save data for one of the currently open acquisitions
propertiesChangedAlert() - Method in interface org.micromanager.api.MMListenerInterface
 
PropertiesChangedEvent - Class in org.micromanager.api.events
 
PropertiesChangedEvent() - Constructor for class org.micromanager.api.events.PropertiesChangedEvent
 
propertyChangedAlert(String, String, String) - Method in interface org.micromanager.api.MMListenerInterface
 
PropertyChangedEvent - Class in org.micromanager.api.events
 
PropertyChangedEvent(String, String, String) - Constructor for class org.micromanager.api.events.PropertyChangedEvent
 
putImage(TaggedImage) - Method in interface org.micromanager.api.TaggedImageStorage
 

R

refreshGUI() - Method in interface org.micromanager.api.ScriptInterface
Brings GUI up to date with the recent changes in the mmcore.
refreshGUIFromCache() - Method in interface org.micromanager.api.ScriptInterface
Brings GUI up to date with the recent changes in the mmcore.
registerForEvents(Object) - Method in interface org.micromanager.api.ScriptInterface
Request that the given object be added to our EventBus for notification of events occurring.
registerProcessorClass(Class<? extends DataProcessor<TaggedImage>>, String) - Method in interface org.micromanager.api.ScriptInterface
Register a new DataProcessor class with the Acquisition Engine.
relativeZSlice - Variable in class org.micromanager.api.SequenceSettings
 
remove(StagePosition) - Method in class org.micromanager.api.MultiStagePosition
 
removeChangeListener(ChangeListener) - Method in class org.micromanager.api.PositionList
 
removeImageCacheListener(ImageCacheListener) - Method in interface org.micromanager.api.ImageCache
Removes an imageCacheListener so that it will no longer be notified of relevant events.
removeImageProcessor(DataProcessor<TaggedImage>) - Method in interface org.micromanager.api.ScriptInterface
Removes an image processor from the DataProcessor pipeline.
removeMMBackgroundListener(Component) - Method in interface org.micromanager.api.ScriptInterface
Lets Components remove themselves from the list whose background gets changed by the Micro-Manager UI.
removeMMListener(MMListenerInterface) - Method in interface org.micromanager.api.ScriptInterface
Allows MMListeners to remove themselves
removePosition(int) - Method in class org.micromanager.api.PositionList
Removes a specific position based on the index
replacePosition(int, MultiStagePosition) - Method in class org.micromanager.api.PositionList
Replaces position in the list with the new position
requestStop() - Method in class org.micromanager.api.DataProcessor
Request that the data processor stop processing.
restore(String) - Method in class org.micromanager.api.PositionList
Restore object data from the JSON encoded stream.
resume() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
root - Variable in class org.micromanager.api.SequenceSettings
 
run() - Method in class org.micromanager.api.DataProcessor
The run method that causes images to be processed.
run(SequenceSettings) - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
run(SequenceSettings, boolean, PositionList, Autofocus) - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
run(SequenceSettings, boolean) - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
runAcquisition() - Method in interface org.micromanager.api.ScriptInterface
Executes Acquisition with current settings Will open the Acquisition Dialog when it is not open yet Returns after Acquisition finishes Note that this function should not be executed on the EDT (which is the thread running the UI).
runAcquisition(String, String) - Method in interface org.micromanager.api.ScriptInterface
Executes Acquisition with current settings but allows for changing the data path.

S

save(String) - Method in class org.micromanager.api.PositionList
Save list to a file.
save - Variable in class org.micromanager.api.SequenceSettings
 
saveAs(TaggedImageStorage) - Method in interface org.micromanager.api.ImageCache
Save a new copy of a TaggedImage data set, stored in a TaggedImageStorage object.
saveAs(TaggedImageStorage, boolean) - Method in interface org.micromanager.api.ImageCache
Save a new copy of a TaggedImage data set, stored in a TaggedImageStorage object.
saveConfigPresets() - Method in interface org.micromanager.api.ScriptInterface
Save current configuration
saveSettings() - Method in interface org.micromanager.api.Autofocus
 
ScriptInterface - Interface in org.micromanager.api
Interface to execute commands in the main panel.
SequenceSettings - Class in org.micromanager.api
 
SequenceSettings() - Constructor for class org.micromanager.api.SequenceSettings
 
serialize() - Method in class org.micromanager.api.PositionList
Serialize object into the JSON encoded stream.
setAcquisitionAddImageAsynchronous(String) - Method in interface org.micromanager.api.ScriptInterface
Change an acquisition so that adding images to it is done asynchronously.
setAcquisitionProperty(String, String, String) - Method in interface org.micromanager.api.ScriptInterface
Sets custom property attached to the acquisition summary
setAcquisitionSettings(SequenceSettings) - Method in interface org.micromanager.api.ScriptInterface
Apply new acquisition settings
setApp(ScriptInterface) - Method in interface org.micromanager.api.Autofocus
 
setApp(ScriptInterface) - Method in class org.micromanager.api.DataProcessor
Receive the ScriptInterface object.
setApp(ScriptInterface) - Method in interface org.micromanager.api.MMPlugin
The main app passes its ScriptInterface to the module.
setBackgroundStyle(String) - Method in interface org.micromanager.api.ScriptInterface
Sets the background color of the GUI and all its registered components to the selected backGroundType
setChannelColor(int, int) - Method in interface org.micromanager.api.ImageCache
Sets the preferred display color for a channel
setChannelColor(String, int, Color) - Method in interface org.micromanager.api.ScriptInterface
Sets the color of the specified channel in the image viewer.
setChannelContrast(String, int, int, int) - Method in interface org.micromanager.api.ScriptInterface
Sets min (black) and max (white or the channel's color) pixel value clipping levels for each channel.
setChannelExposureTime(String, String, double) - Method in interface org.micromanager.api.ScriptInterface
Updates the exposure time associated with the given preset If the channelgroup and channel name match the current state the exposure time will also be updated
setChannelName(String, int, String) - Method in interface org.micromanager.api.ScriptInterface
Sets the channel name (label)
setComment(String) - Method in interface org.micromanager.api.ImageCache
Set the data set's comment string for this image cache.
setConfigChanged(boolean) - Method in interface org.micromanager.api.ScriptInterface
lets the GUI know that the current configuration has been changed.
setContrastBasedOnFrame(String, int, int) - Method in interface org.micromanager.api.ScriptInterface
Autoscales contrast for each channel at the current position based on pixel values at the current slice and frame
setDefaultXYStage(String) - Method in class org.micromanager.api.MultiStagePosition
Defines which stage serves as the XY motion control device
setDefaultZStage(String) - Method in class org.micromanager.api.MultiStagePosition
Defines which stage serves as focus control
setDisplayAndComments(JSONObject) - Method in interface org.micromanager.api.TaggedImageStorage
 
setEnabled(boolean) - Method in class org.micromanager.api.DataProcessor
Turn the Processor on or off.
setGridCoordinates(int, int) - Method in class org.micromanager.api.MultiStagePosition
Sets grid parameters for the rectangular grid
setImageComment(String, JSONObject) - Method in interface org.micromanager.api.ImageCache
Set the comment string for an individual image.
setImageProcessorPipeline(List<DataProcessor<TaggedImage>>) - Method in interface org.micromanager.api.ScriptInterface
Replace the current DataProcessor pipeline with the provided one.
setImageProperty(String, int, int, int, String, String) - Method in interface org.micromanager.api.ScriptInterface
Sets property attached to an individual image.
setImageSavingFormat(Class) - Method in interface org.micromanager.api.ScriptInterface
Set the format for saving images to disk.
setInput(BlockingQueue<E>) - Method in class org.micromanager.api.DataProcessor
Sets the input queue where objects to be processed are received by the DataProcessor.
setLabel(String) - Method in class org.micromanager.api.MultiStagePosition
Sets position label (such as well name, etc.)
setLabel(int, String) - Method in class org.micromanager.api.PositionList
Assigns a label to the position index
setOutput(BlockingQueue<E>) - Method in class org.micromanager.api.DataProcessor
Sets the output queue where objects that have been processed exit the DataProcessor.
setPause(boolean) - Method in interface org.micromanager.api.ScriptInterface
Pause/Unpause a running acquistion
setPosition(int) - Method in class org.micromanager.api.MMWindow
Sets the display to the given position Position are 1-based
setPositionList(PositionList) - Method in interface org.micromanager.api.ScriptInterface
Makes this the 'current' PositionList, i.e., the one used by the Acquisition Protocol Replaces the list in the PositionList Window It will open a position list dialog if it was not already open.
setPositions(MultiStagePosition[]) - Method in class org.micromanager.api.PositionList
Initialize the entire array by passing an array of multi-stage positions
setProperty(PropertyItem) - Method in interface org.micromanager.api.Autofocus
 
setProperty(String, String) - Method in class org.micromanager.api.MultiStagePosition
Add a generalized property-value par to the position.
setPropertyValue(String, String) - Method in interface org.micromanager.api.Autofocus
 
setRelativeStagePosition(double) - Method in interface org.micromanager.api.ScriptInterface
Move default Focus (Z) relative to current position and block until done
setRelativeXYStagePosition(double, double) - Method in interface org.micromanager.api.ScriptInterface
Move default XY stage relative to current position and block until done.
setROI(Rectangle) - Method in interface org.micromanager.api.ScriptInterface
Set the default camera's ROI -- a convenience function.
setStagePosition(double) - Method in interface org.micromanager.api.ScriptInterface
Move default Focus (Z) and block until done
setSummaryMetadata(JSONObject) - Method in interface org.micromanager.api.TaggedImageStorage
 
setXYOrigin(double, double) - Method in interface org.micromanager.api.ScriptInterface
Assigns the current stage position of the default xy-stage to be (x,y), thereby offseting the coordinates of all other positions.
setXYStagePosition(double, double) - Method in interface org.micromanager.api.ScriptInterface
Move default XY stage and block until done.
show() - Method in interface org.micromanager.api.MMPlugin
Open the module window
showAutofocusDialog() - Method in interface org.micromanager.api.ScriptInterface
Shows the dialog with options for the currently active autofocus device.
showError(Exception, String) - Method in interface org.micromanager.api.ScriptInterface
Shows an error in the UI and logs stacktrace to the Micro-Manager log.
showError(Exception) - Method in interface org.micromanager.api.ScriptInterface
Shows and logs a Java exception.
showError(String) - Method in interface org.micromanager.api.ScriptInterface
Shows an error message in the UI and logs to the Micro-Manager log.
showError(Exception, String, Component) - Method in interface org.micromanager.api.ScriptInterface
Shows an error in the UI and logs stacktrace to the Micro-Manager log.
showError(Exception, Component) - Method in interface org.micromanager.api.ScriptInterface
Shows and logs a Java exception.
showError(String, Component) - Method in interface org.micromanager.api.ScriptInterface
Shows an error message in the UI and logs to the Micro-Manager log.
showMessage(String) - Method in interface org.micromanager.api.ScriptInterface
Shows a message in the UI.
showMessage(String, Component) - Method in interface org.micromanager.api.ScriptInterface
Shows a message in the UI.
showXYPositionList() - Method in interface org.micromanager.api.ScriptInterface
shows the position list dialog
size() - Method in class org.micromanager.api.MultiStagePosition
Number of stages.
skipAutofocusCount - Variable in class org.micromanager.api.SequenceSettings
 
sleep(long) - Method in interface org.micromanager.api.ScriptInterface
Request a pause in script execution for the specified number of milliseconds.
SLICE - Static variable in class org.micromanager.api.MMTags.Image
 
SLICE_INDEX - Static variable in class org.micromanager.api.MMTags.Image
 
SLICES - Static variable in class org.micromanager.api.MMTags.Summary
 
slices - Variable in class org.micromanager.api.SequenceSettings
 
SLICES_FIRST - Static variable in class org.micromanager.api.MMTags.Summary
 
slicesFirst - Variable in class org.micromanager.api.SequenceSettings
 
slmExposureChanged(String, double) - Method in interface org.micromanager.api.MMListenerInterface
Implement to be notified that the exposure time given camera has changed
SLMExposureChangedEvent - Class in org.micromanager.api.events
 
SLMExposureChangedEvent(String, double) - Constructor for class org.micromanager.api.events.SLMExposureChangedEvent
 
snapAndAddImage(String, int, int, int, int) - Method in interface org.micromanager.api.ScriptInterface
Snaps an image with the current settings and places pixels in the specified position of the Micro-Manager Image viewer
snapSingleImage() - Method in interface org.micromanager.api.ScriptInterface
Snaps image and displays in AcqWindow.
SOURCE - Static variable in class org.micromanager.api.MMTags.Summary
 
stageName - Variable in class org.micromanager.api.StagePosition
 
StagePosition - Class in org.micromanager.api
 
StagePosition() - Constructor for class org.micromanager.api.StagePosition
 
stagePositionChangedAlert(String, double) - Method in interface org.micromanager.api.MMListenerInterface
 
StagePositionChangedEvent - Class in org.micromanager.api.events
 
StagePositionChangedEvent(String, double) - Constructor for class org.micromanager.api.events.StagePositionChangedEvent
 
stop() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
stopHasBeenRequested() - Method in interface org.micromanager.api.IAcquisitionEngine2010
 
storagePluginName - Static variable in interface org.micromanager.api.TaggedImageStorage
 
storeChannelDisplaySettings(int, int, int, double, int, int) - Method in interface org.micromanager.api.ImageCache
Store the display settings for a particular channel.
SUMMARY - Static variable in class org.micromanager.api.MMTags.Root
 
systemConfigurationLoaded() - Method in interface org.micromanager.api.MMListenerInterface
This function will be called when a configuration file is loaded It can be used to stay informed of changes in the hardware configuration Note that devices can be loaded an unloaded individually, in which case this function will not be called
SystemConfigurationLoadedEvent - Class in org.micromanager.api.events
 
SystemConfigurationLoadedEvent() - Constructor for class org.micromanager.api.events.SystemConfigurationLoadedEvent
 

T

TaggedImageAnalyzer - Class in org.micromanager.api
This class is used to analyze (but not modify images).
TaggedImageAnalyzer() - Constructor for class org.micromanager.api.TaggedImageAnalyzer
 
TaggedImageStorage - Interface in org.micromanager.api
This interface is implemented by TaggedImageStorage classes.
TIME - Static variable in class org.micromanager.api.MMTags.Image
 
TIME_FIRST - Static variable in class org.micromanager.api.MMTags.Summary
 
timeFirst - Variable in class org.micromanager.api.SequenceSettings
 
toJSONStream(SequenceSettings) - Static method in class org.micromanager.api.SequenceSettings
 

U

unregisterForEvents(Object) - Method in interface org.micromanager.api.ScriptInterface
Unregister the given object from EventBus notfications
useAutofocus - Variable in class org.micromanager.api.SequenceSettings
 
usePositionList - Variable in class org.micromanager.api.SequenceSettings
 

V

Version - Static variable in class org.micromanager.api.SequenceSettings
 
versionLessThan(String) - Method in interface org.micromanager.api.ScriptInterface
Displays an error message and returns true if the run-time Micro-Manager version is less than the one specified.

W

WIDTH - Static variable in class org.micromanager.api.MMTags.Image
 
WIDTH - Static variable in class org.micromanager.api.MMTags.Summary
 
writeDisplaySettings() - Method in interface org.micromanager.api.TaggedImageStorage
 

X

x - Variable in class org.micromanager.api.StagePosition
NOTE: despite what the name fields in this class may suggest, every StagePosition in practice has only 1 or 2 axes, and thus only uses either the x, or the x and y fields.
XUM - Static variable in class org.micromanager.api.MMTags.Image
 
xyStagePositionChanged(String, double, double) - Method in interface org.micromanager.api.MMListenerInterface
 
XYStagePositionChangedEvent - Class in org.micromanager.api.events
 
XYStagePositionChangedEvent(String, double, double) - Constructor for class org.micromanager.api.events.XYStagePositionChangedEvent
 

Y

y - Variable in class org.micromanager.api.StagePosition
 
YUM - Static variable in class org.micromanager.api.MMTags.Image
 

Z

z - Variable in class org.micromanager.api.StagePosition
 
zReference - Variable in class org.micromanager.api.SequenceSettings
 
ZUM - Static variable in class org.micromanager.api.MMTags.Image
 
A B C D E F G H I K L M N O P R S T U V W X Y Z