main controller for MIB More...

Inheritance diagram for mibController:

Collaboration diagram for mibController:

Public Member Functions
function	devTest_ClickedCallback ()
	for developmental purposes

function	exitProgram ()
	Executes when user attempts to close MIB.

function id =	findChildId (childName)
	find id of a child controller

function	getDefaultParameters ()
	Set default or/and stored from a previous session parameters of MIB.

function	imageRedraw ()
	redraw image in the handles.mibImageAxes after press of handles.mibHideImageCheck or transparency sliders

function result =	menuDatasetParameters_Callback (pixSize, BatchOptIn)
	a callback for MIB->Menu->Dataset->Parameters

function	menuDatasetScalebar_Callback (parameter)
	a callback to Menu->Dataset->Scale bar calibrate pixel size from an existing scale bar

function	menuDatasetSlice_Callback (parameter)
	a callback to Menu->Dataset->Slice do actions with individual slices

function	menuDatasetTrasform_Callback (mode, BatchOpt)
	a callback to Menu->Dataset->Transform... do different transformation with the dataset

function	menuFileChoppedImage_Callback (parameter)
	a callback to Menu->File->Chopped images, chop/rechop dataset to/from smaller subsets

function	menuFileExamples_Callback (parameter)
	a callback to Menu->File->Example datasets, import an example dataset into MIB

function	menuFileExportImage_Callback (parameter)
	a callback to Menu->File->Export Image, export image and meta-data from MIB to the main Matlab workspace or Imaris

function	menuFileImportImage_Callback (parameter)
	a callback to Menu->File->Import Image, import image from Matlab main workspace or system clipboard

function	menuFilePreference_Callback ()
	a callback to MIB->Menu->File->Preferences...

function	menuFileRender_Callback (parameter)
	a callback to MIB->Menu->File->Render volume...

function	menuFileSaveImageAs_Callback ()
	a callback to the mibGUI.handles.menuFileSaveImageAs, saves image to a file

function	menuImageColorCh_Callback (parameter)
	callback to Menu->Image->Color Channels do actions with individual color channels

function	menuImageContrast_Callback (parameter)
	a callback to Menu->Image->Contrast; do contrast enhancement

function	menuImageIntensity_Callback (parameter)
	callback to the Menu->Image->Intensity profile; get the image intensity profile

function	menuImageInvert_Callback (mode, BatchOptIn)
	callback for Menu->Image->Invert image; start invert image

function status =	menuImageMode_Callback (hObject, BatchOpt)
	callback to the Menu->Image->Mode, convert image to different formats

function	menuImageToolsProjection_Callback (BatchOptIn)
	callback to the Menu->Image->Tools->Intensity projection, calculate intensity projection of the dataset

function	menuMaskExport_Callback (ExportTo, BatchOptIn)
	callback to Menu->Mask->Export, export the Mask layer to Matlab or another buffer

function	menuMaskImageReplace_Callback (type, BatchOptIn)
	callback to Menu->Mask->Replace color; Replace image intensities in the Masked or Selected areas with new intensity value

function	menuMaskImport_Callback (ImportFrom, BatchOptIn)
	callback to Menu->Mask->Import, import the Mask layer from Matlab or another buffer of MIB

function	menuMaskInvert_Callback (type, BatchOptIn)
	callback to Menu->Mask->Invert; invert the Mask/Selection layer

function	menuMaskLoad_Callback ()
	callback to Menu->Mask->Load Mask; load the Mask layer to MIB from a file

function	menuMaskSaveAs_Callback ()
	callback to Menu->Mask->Save As; save the Mask layer to a file

function	menuModelAnn_Callback (parameter)
	callback to Menu->Models->Annotations

function	menuModelsExport_Callback (exportTo)
	callback to Menu->Models->Export export the Model layer to the main Matlab workspace

function	menuModelsImport_Callback (BatchOptIn)
	callback to Menu->Models->Import; import the Model layer from the main Matlab workspace

function	menuModelsRender_Callback (type)
	a callback to MIB->Menu->Models->Render model...

function	menuModelsSaveAs_Callback (parameter)
	callback to Menu->Models->Save as save model to a file

function	menuSelectionBuffer_Callback (parameter)
	a callback to Menu->Selection to Buffer... to Copy/Paste/Clear of the selection of the shown layer

function	menuSelectionInterpolate ()
	a callback to the Menu->Selection->Interpolate; interpolates shapes of the selection layer

function	menuSelectionToMaskBorder_Callback ()
	callback to Menu->Selection->Expand to Mask border expand selection to borders of the Masked layer

function	menuToolsMeasure_Callback (type)
	a callback for selection of obj.mibView.handles.menuToolsMeasure entries

function	mibAddMaterialBtn_Callback (BatchOptIn)
	callback to the obj.mibView.handles.mibAddMaterialBtn, add material to the model

function	mibAnisotropicDiffusion (filter_type, cpuParallelLimit)
	Filter image with Anisotropic diffusion filters.

function	mibAnnMarkerEdit_Callback ()
	callback for selection of annotation marker type, updates mibAnnMarkerEdit field of the mibModel

function	mibAutoBrightnessBtn_Callback ()
	Adjust brightness automatically for the shown image.

function	mibBioformatsCheck_Callback ()
	Bioformats that can be read with loci BioFormats toolbox this function updates the list of file filters in obj.mibView.handles.mibFileFilterPopup.

function	mibBufferToggle_Callback (Id, BatchOptIn)
	a callback to press of obj.mibView.handles.mibBufferToggle button

function	mibBufferToggleContext_Callback (parameter, buttonID, BatchOptIn)
	callback function for the popup menu of the buffer buttons in the upper part of the Directory contents panel. This callback is triggered from all those buttons.

function	mibBrushPanelInterpolationSettingsBtn_Callback ()
	mibBrushPanelInterpolationSettingsBtn_Callback(obj, hObject) callback for modification of superpixel mode settings of the brush tool

function	mibBrushSuperpixelsEdit_Callback (hObject)
	mibBrushSuperpixelsEdit_Callback(obj, hObject) callback for modification of superpixel mode settings of the brush tool

function	mibBrushSuperpixelsWatershedCheck_Callback (hObject)
	mibBrushSuperpixelsWatershedCheck_Callback(obj, hObject) callback for selection of superpixel mode for the brush tool

function	mibChangeLayerEdit_Callback (parameter, BatchOptIn)
	A callback for changing the slices of the 3D dataset by entering a new slice number.

function	mibChangeLayerSlider_Callback ()
	A callback function for mibGUI.mibChangeLayerSlider. Responsible for showing next or previous slice of the dataset.

function	mibChangeTimeEdit_Callback (parameter, BatchOptIn)
	A callback for changing the time points of the dataset by entering a new time value.

function	mibChangeTimeSlider_Callback ()
	A callback function for mibGUI.mibChangeTimeSlider. Responsible for showing next or previous time point of the dataset.

function	mibChannelMixerTable_Callback (type)
	a callback for the context menu of obj.mibView.handles.mibChannelMixerTable

function	mibChannelMixerTable_CellEditCallback (Indices, PreviousData, modifier)
	a callback edit of a cell in obj.mibView.handles.mibChannelMixerTable

function	mibChannelMixerTable_CellSelectionCallback (Indices)
	a callback selection of a cell in obj.mibView.handles.mibChannelMixerTable

function	mibColChannelCombo_Callback ()
	callback for modification of obj.View.handles.mibColorChannelCombo box

function	mibCreateModelBtn_Callback ()
	Create a new model, callback for press of the Create button in mibGUI.

function	mibDoUndo (newIndex)
	Undo the recent changes with Ctrl+Z shortcut.

function	mibDragAndDropFiles (DragNDrop, event)
	callback for dropping the files into the image view panel: loading the files

function	mibDragAndDropModelFiles (DragNDrop, event)
	callback for dropping model files into the segmentation table: loading the files

function	mibEraserEdit_Callback ()
	increase size of the eraser tool with the provided in obj.mibView.handles.mibEraserEdit

function	mibFijiExport ()
	Export currently open dataset to Fiji.

function	mibFijiImport ()
	import dataset from Fiji to MIB

function	mibFijiRunMacro ()
	run command or macro on Fiji

function	mibFileFilterPopup_cm (parameter)
	a context menu to the to the handles.mibFileFilterPopup, the menu is called with the right mouse button

function	mibFilesListbox_Callback ()
	navigation in the file list, i.e. open file or change directory

function	mibFilesListbox_cm_Callback (parameter, BatchOptIn)
	a context menu to the to the handles.mibFilesListbox, the menu is called with the right mouse button

function	mibFindMaterialUnderCursor ()
	find material under the mouse cursor, a callback for Ctrl+F key shortcut

function	mibImageFilterDoitBtn_Callback ()
	a callback to the obj.mibView.handles.mibImageFilterDoitBtn, apply image filtering using the selected filter

function	menuImageToolsContentAware_Callback ()
	callback to the Menu->Image->Tools->Content-aware fill, fill the selected area using content aware algorithms

function	mibLoadModelBtn_Callback ()
	callback to the obj.mibView.handles.mibLoadModelBtn, loads model to MIB from a file

function	mibMaskedAreaCheck_Callback ()
	a callback to the mibGUI.handles.mibMaskedAreaCheck, allows to toggle state of the `Masked area`

function	mibMaskGenerator (type)
	generate the `Mask` later

function	mibMaskRecalcStatsBtn_Callback ()
	recalculate objects for Mask or Model layer to use with the Object Picker tool in 3D

function	mibMaskShowCheck_Callback ()
	a callback to the mibGUI.handles.maskShowCheck, allows to toggle visualization of the mask layer

function	mibModelPropertyUpdate (parameter)
	% update switches in the obj.mibModel class that describe states of GUI widgets

function meta =	getMeta ()
	get meta data for the currently shown dataset, mibImage.meta

function	mibLutCheckbox_Callback ()
	a callback to the mibGUI.handles.mibLutCheckbox, turn on/off visualization of color channels using luck-up table (LUT)

function	mibModelShowCheck_Callback ()
	callback to the mibGUI.handles.mibModelShowCheck to toggle the Model layer on/off

function	mibPixelInfo_Callback (parameter, BatchOptIn)
	center image to defined position it is a callback from a popup menu above the pixel information field of the Path panel

function	mibRecolorLabels ()
	recolor color map for 65535+ models

function	mibRemoveMaterialBtn_Callback (BatchOptIn)
	callback to the obj.mibView.handles.mibRemoveMaterialBtn, remove material from the model

function	mibRoiAddBtn_Callback ()
	a callback to handles.mibRoiAddBtn, adds a roi to a dataset

function	mibRoiList_cm_Callback (parameter)
	a callback for obj.mibView.handles.mibRoiList context menu

function	mibRoiLoadBtn_Callback ()
	a callback to the obj.mibView.handles.mibRoiLoadBtn, loads roi from a file to MIB

function	mibRoiOptionsBtn_Callback (parameter)
	update ROI visualization settings, as callback of mibGUI.handles.mibRoiOptionsBtn

function	mibRoiRemoveBtn_Callback ()
	a callback to obj.mibView.handles.mibRoiRemoveBtn, remore selected ROI

function	mibRoiSaveBtn_Callback ()
	a callback to the obj.mibView.handles.mibRoiSaveBtn, saves roi to a file in the matlab format

function	mibRoiShowCheck_Callback (parameter)
	toggle show/hide state of ROIs, as callback of mibGUI.handles.mibRoiShowCheck

function	mibRoiToSelectionBtn_Callback ()
	a callback to obj.mibView.handles.mibRoiToSelectionBtn, highlight area under the selected ROI in the Selection layer

function	mibSegmentation3dBall (y, x, z, modifier, BatchOptIn)
	Do segmentation using the 3D ball tool.

function	mibSegmentationAnnotation (y, x, z, t, modifier, options)
	Add text annotation to the dataset.

function	mibSegmAnnDeleteAllBtn_Callback ()
	callback to Menu->Models->Annotations...->Delete all annotations, delete all annotations of the model

function	mibSegmentationBlackWhiteThreshold (parameter, BatchOptIn)
	Perform black and white thresholding for BW Threshold tool of the 'Segmentation panel'.

function	mibSegmentationBrush (y, x, modifier)
	mibSegmentation_Brush(obj, y, x, modifier) Do segmentation using the brush tool

function	mibSegmentationDragAndDrop (y, x, modifier)
	mibSegmentationDragAndDrop(y, x, modifier) Fix segmentation or mask/selection layers by dragging individual 2D/3D objects or complete models with a mouse

function	mibSegmentationLasso (modifier)
	Do segmentation using the lasso tool.

function	mibSegmentationLassoManual (modifier)
	Do manual segmentation using the lasso tool in the manual mode.

function	mibSegmentationLines3D (y, x, z, modifier)
	output = mibSegmentationLines3D(obj, y, x, z, modifier) Add and modify 3D lines

function	mibSegmentationMagicWand (yxzCoordinate, modifier)
	Do segmentation using the Magic Wand tool.

function output =	mibSegmentationMembraneClickTraker (yxzCoordinate, yx, modifier)
	output = mibSegmentationMembraneClickTraker(obj, yxzCoordinate, yx, modifier) Trace membranes and draw a straight lines in 2d and 3d

function	mibSegmentationObjectPicker (yxzCoordinate, modifier)
	Select 2d/3d objects from the Mask or Model layers.

function	mibSegmentationPanelCheckboxes (BatchOptIn)
	a function of the batch mode that allow to tweak the status of checkboxes of the Segmentation panel

function	mibSegmentationRegionGrowing (yxzCoordinate, modifier)
	Do segmentation using the Region Growing method.

function	mibSegmentationSAM (extraOptions, BatchOptIn)
	Perform segmentation using segment-anything model https://segment-anything.com.

function	mibSegmentationSAM2 (extraOptions, BatchOptIn)
	Perform segmentation using segment-anything-2 model https://github.com/facebookresearch/segment-anything-2.

function status =	mibSegmentationSAM_requirements (samVersion)
	Check for files required to run segmentation using segment-anything model https://segment-anything.com.

function	mibSegmentationSpot (y, x, modifier, BatchOptIn)
	mibSegmentationSpot(obj, y, x, modifier, BatchOptIn) Do segmentation using the spot tool

function	mibSegmentationTable_CellSelectionCallback (eventdata)
	mibSegmentationTable_CellSelectionCallback(obj, eventdata) Callback for cell selection in the handles.mibSegmentationTable table of mibGIU.m

function	mibSegmentationTable_cm_Callback (hObject, type)
	a callback to the context menu of mibView.handles.mibSegmentationTable

function	mibSegmentationToolPopup_Callback ()
	a callback to the handles.mibSegmentationToolPopup, allows to select tool for the segmentation

function	mibSegmFavToolCheck_Callback ()
	callback to the obj.mibView.handles.mibSegmFavToolCheck, to add the selected tool to the list of favourites

function	mibSegmSAMPanel_Callbacks (tag)
	callbacks for widgets of obj.mibView.handles.mibSegmSAMPanel

function	mibSegmSelectedOnlyCheck_Callback ()
	a callback to the mibGUI.handles.mibSegmSelectedOnlyCheck, allows to toggle state of the `Fix selection to material`

function	mibSelectionButton_Callback (action)
	a callback to `A`, `S`, `R` buttons in the Selection panel of obj.mibView.gui

function	mibSelectionClearBtn_Callback ()
	a callback to the mibGUI.handles.mibSelectionClearBtn, allows to clear the Selection layer

function	mibSelectionDilateBtn_Callback ()
	a callback to the mibGUI.handles.mibSelectionDilateBtn, expands the selection layer

function	mibSelectionErodeBtn_Callback ()
	a callback to the mibGUI.handles.mibSelectionErodeBtn, shrinks the selection layer

function	mibSelectionFillBtn_Callback ()
	a callback to the mibGUI.handles.mibSelectionFillBtn, allows to fill holes for the Selection layer

function	mibSelectionPanelCheckboxes (BatchOptIn)
	a function of the batch mode that allow to tweak the status of checkboxes of the Selection panel

function	mibShowMilestoneDialog (mode)
	show a milestone dialog with user performance and stats

function	mibToolbar_ZoomBtn_ClickedCallback (hObject, recenterSwitch)
	modifies magnification using the zoom buttons in the toolbar of MIB

function	mibToolbarPlaneToggle (hObject, moveMouseSw)
	a callback to the change orientation buttons in the toolbar of MIB; it toggles viewing plane: xy, zx, or zy direction

function	mibUpdatePresetFromSegmentationSettings (presetId)
	update preset using the current settings of the selected segmentation tool; this function is a callback on press of Shift+1, Shift+2, Shift+3 default key shortcuts

function	mibUpdateSegmentationSettingsFromPreset (presetId)
	update settings of the selected segmentation tool from preset, this function is a callback on press of 1,2,3 default key shortcuts

function	mibViewSettingsPanelCheckboxes (BatchOptIn)
	a function of the batch mode that allow to tweak status of checkboxes of the View Settings panel

function	mibZoomEdit_Callback (BatchOptIn)
	callback function for modification of the handles.mibZoomEdit

function	mibGUI_Brush_scrollWheelFcn (eventdata)
	Control callbacks from mouse scroll wheel during the brush tool.

function	mibGUI_panAxesFcn (xy, imgWidth, imgHeight)
	This function is responsible for moving image in obj.mibView.handles.mibImageAxes during panning.

function	mibGUI_PanelShiftBtnUpFcn (panelName)
	callback for the release of a mouse button over handles.mibSeparatingPanel to change size of Directory contents and Segmentation panels

function	mibGUI_ScrollWheelFcn (eventdata)
	Control callbacks from mouse scroll wheel.

function	mibGUI_SizeChangedFcn (resizeParameters)
	resizing for panels of MIB

function	mibGUI_WindowBrushMotionFcn (selection_layer, structElement, currMask)
	This function draws the brush trace during use of the brush tool.

function	mibGUI_WindowButtonDownFcn ()
	this is callback for the press of a mouse button

function	mibGUI_WindowButtonUpFcn (brush_switch)
	callback for release of the mouse button

function	mibGUI_WindowButtonUpDragAndDropFcn (mode, diffX, diffY, BatchOptIn)
	callback for release of the mouse button after use of the Drag and Drop materials tool

function	mibGUI_WindowDragAndDropMotionFcn (selection_layer)
	This function draws the displaced materials during use of the drag and drop materials tool.

function	mibGUI_WindowKeyPressFcn (hObject, eventdata)
	callback for a key press in mibGUI

function	mibGUI_WindowKeyPressFcn_BrushSuperpixel (eventdata)
	a function to check key callbacks when using the Brush in the Superpixel mode

function	mibGUI_WindowKeyReleaseFcn (eventdata)
	callback for release of keys in mibGUI window

function	mibGUI_WinMouseMotionFcn ()
	returns coordinates and image intensities under the mouse cursor

function	plotImage (resize, sImgIn)
	Plot image to mibImageAxes. The main drawing function.

function	redrawMibChannelMixerTable ()
	Update obj.mibView.handles.mibChannelMixerTable table and obj.mibView.handles.mibColChannelCombo color combo box.

function	setMeta (meta)
	set meta data for the currently shown dataset, mibImage.meta

function	startController (controllerName, varargin)
	start a child controller using provided name

function	startPlugin (pluginName)
	start plugin from MIB menu

function	toolbarBlockModeSwitch_ClickedCallback ()
	a callback for press of obj.mibView.toolbarBlockModeSwitch in the toolbar of MIB

function	toolbarCenterPointShow_ClickedCallback ()
	a callback for press of obj.mibView.toolbarCenterPointShow in the toolbar of MIB. Toggles display of a center point over the mibImageAxis

function	toolbarInterpolation_ClickedCallback (options)
	Function to set the state of the interpolation button in the toolbar.

function	toolbarRedo_ClickedCallback ()
	do one step forward in the undo history

function	toolbarResizingMethod_ClickedCallback (options)
	Function to set type of image interpolation for the visualization.

function	toolbarUndo_ClickedCallback ()
	do one step back in the undo history

function newMode =	toolbarVirtualMode_ClickedCallback (options)
	Function to switch between loading datasets to memory or reading them from HDD on demand.

function	updateAxesLimits (index, mode, newMagFactor)
	Updates the obj.mibImage.axesX and obj.mibImage.axesY during fit screen, resize, or new dataset drawing.

function	updateFilelist (filename)
	Update list of files in the current working directory (obj.mibModel.myPath)

function	updateGuiWidgets ()
	Update user interface widgets in obj.mibView.gui based on the properties of the opened dataset.

function	updateMyPath (myPath)
	update mibModel.myPath, which is the current working directory

function	updateShownId (Id)
	update index of the displayed dataset, after, for example press of the handles.mibBufferToggle buttons in mibGUI

function	updateSegmentationTable (position)
	Update obj.mibView.handles.mibSegmentationTable in the main window of mibGIU.m.

function	volrenToolbarSwitch_ClickedCallback (parameter)
	a callback for press of obj.mibView.volrenToolbarSwitch in the toolbar of MIB

function	volren_WindowButtonDownFcn ()
	callback for the press of a mouse button during the volume rendering mode

function	volren_scrollWheelFcn (eventdata)
	callback for mouse wheel during the volume rendering mode

function	volren_winMouseMotionFcn ()
	change cursor shape when cursor is inside the axis during the volume rendering mode

function	volren_WindowButtonUpFcn ()
	callback for mouse button up event during the volume rendering mode

function	volren_WindowInteractMotionFcn (seltype)
	callback for translation/rotation of dataset during the volume rendering mode

	mibController (mibModel, mibVersion)
	mibController class constructor

Static Public Member Functions
static function	purgeControllers (obj, src, evnt)
	> Description of events find index of the child controller

static function	listner_ModelEvent_Callback (obj, src, evnt)
	callback function for detection of mibModel callbacks this function is recommended to use

static function	Listner2_Callback (obj, src, evnt)

Public Attributes
	mibVersion
	= `ver. 2.601 / 04.11.2019`; % ATTENTION! it is important to have the version number between "ver." and "/" version of MIB

	mibVersionNumeric
	version of MIB in numerical form

	mibModel
	handles to the model

	mibView
	handle to the view

	listener
	a cell array with handles to listeners

	matlabVersion
	version of Matlab

	mibPath
	path to MIB installation directory

	DragNDrop
	drag and drop handle for dropping the files to the file listbox

	DragNDropModel
	drag and drop handle for dropping the files to the file listbox

	brushSizeNumbers
	matrix with the font for changing of brush size

	childControllers
	list of opened subcontrollers

	childControllersIds
	a cell array with names of initialized child controllers

Public Attributes inherited from handle
	addlistener
	Creates a listener for the specified event and assigns a callback function to execute when the event occurs.

	notify
	Broadcast a notice that a specific event is occurring on a specified handle object or array of handle objects.

	delete
	Handle object destructor method that is called when the object's lifecycle ends.

	disp
	Handle object disp method which is called by the display method. See the MATLAB disp function.

	display
	Handle object display method called when MATLAB software interprets an expression returning a handle object that is not terminated by a semicolon. See the MATLAB display function.

	findobj
	Finds objects matching the specified conditions from the input array of handle objects.

	findprop
	Returns a meta.property objects associated with the specified property name.

	fields
	Returns a cell array of string containing the names of public properties.

	fieldnames
	Returns a cell array of string containing the names of public properties. See the MATLAB fieldnames function.

	isvalid
	Returns a logical array in which elements are true if the corresponding elements in the input array are valid handles. This method is Sealed so you cannot override it in a handle subclass.

	eq
	Relational functions example. See details for more information.

	transpose
	Transposes the elements of the handle object array.

	permute
	Rearranges the dimensions of the handle object array. See the MATLAB permute function.

	reshape
	hanges the dimensions of the handle object array to the specified dimensions. See the MATLAB reshape function.

	sort
	ort the handle objects in any array in ascending or descending order.

Detailed Description

main controller for MIB

Constructor & Destructor Documentation

◆ mibController()

mibController.mibController	(		mibModel,
			mibVersion )

mibController class constructor

Constructor for the mibController class. Create a new instance of the class with default parameters

Parameters

mibModel	a handle to mibModel class
mibVersion	a string with the current version of MIB

References handle.addlistener, findjobj(), mibAddText2Img(), mibController(), mibGetVersionNumberic(), mibModel, mibPath, mibVersion, and mibView.

Referenced by mibController(), and startController().

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Member Function Documentation

◆ devTest_ClickedCallback()

function mibController.devTest_ClickedCallback ( )

for developmental purposes

use for various tests

Examples:

mibController.obj.devTest_ClickedCallback(); // call from mibController; start developer functions

mibController.mibController

mibController(mibModel, mibVersion)

mibController class constructor

Definition mibController.m:567

◆ exitProgram()

function mibController.exitProgram ( )

Executes when user attempts to close MIB.

Examples:

handles.mibController.exitProgram(); // use this function in minGUI

References getPrefDir(), and handle.isvalid.

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◆ findChildId()

function id = mibController.findChildId ( childName )

find id of a child controller

the child controllers of MIB are stored in obj.childControllersIds cell array. This function look for index that matches with childName string. If it is in the list the function returns its index, otherwise it adds it to the list as a new element

Parameters

childName name of a child controller

Return values

id	index of the requested child controller or empty if it is not open

Examples:

id = obj.findChildId('mibImageAdjController'); // find an index of mibImageAdjController

◆ getDefaultParameters()

function mibController.getDefaultParameters ( )

Set default or/and stored from a previous session parameters of MIB.

This function runs during initialization of mibController.m

References handle.disp, getPrefDir(), mibConcatenateStructures(), and mibPath.

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◆ getMeta()

function meta = mibController.getMeta ( )

get meta data for the currently shown dataset, mibImage.meta

Return values

meta	information about the dataset, an instance of the `containers`.`Map` class

Examples:

meta = obj.getMeta(); // Call from mibController: get meta data

◆ imageRedraw()

function mibController.imageRedraw ( )

redraw image in the handles.mibImageAxes after press of handles.mibHideImageCheck or transparency sliders

Return values

◆ Listner2_Callback()

static function mibController.Listner2_Callback	(	obj,
		src,
		evnt )

static

References handle.fieldnames.

◆ listner_ModelEvent_Callback()

static function mibController.listner_ModelEvent_Callback	(	obj,
		src,
		evnt )

static

callback function for detection of mibModel callbacks this function is recommended to use

Required fields of evnt:

Required fields of obj:

References handle.fieldnames.

◆ menuDatasetParameters_Callback()

function result = mibController.menuDatasetParameters_Callback	(		pixSize,
			BatchOptIn )

a callback for MIB->Menu->Dataset->Parameters

Parameters

pixSize

- [optional], a structure with new parameters, may have the following fields

.x - physical voxel size in X, a number
.y - physical voxel size in Y, a number
.z - physical voxel size in Z, a number
.t - time difference between the frames, a number
.units - physical units for voxels, (m, cm, mm, um, nm)
.tunits - time unit

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event

.VoxelX - string, physical voxel size in X
.VoxelY - string, physical voxel size in Y
.VoxelZ - string, physical voxel size in Z
.VoxelT - string, time difference between the frames
.Units - cell string, {m,cm,mm,um,nm} - identifier of physical units
.TimeUnits - string, identifier of time units
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

Required fields of pixSize:

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuDatasetScalebar_Callback()

function mibController.menuDatasetScalebar_Callback ( parameter )

a callback to Menu->Dataset->Scale bar calibrate pixel size from an existing scale bar

References mibInputMultiDlg(), and mibPath.

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◆ menuDatasetSlice_Callback()

function mibController.menuDatasetSlice_Callback ( parameter )

a callback to Menu->Dataset->Slice do actions with individual slices

Parameters

parameter

a string that defines image source:

copySlice, copy slice (a section from a Z-stack) from one position to another
insertSlice, insert an empty slice
deleteSlice, delete slice (a section from a Z-stack) from the dataset
deleteFrame, delete frame (a section from a time series) from the dataset
reslice, strided reslicing the dataset so that the selected slices are kept and all others are removed
swapSlice, swap two or more slices

◆ menuDatasetTrasform_Callback()

function mibController.menuDatasetTrasform_Callback	(		mode,
			BatchOpt )

a callback to Menu->Dataset->Transform... do different transformation with the dataset

Parameters

mode

a string with a transormation mode:

Add frame (width/height), add a frame around the dataset by providing new width and height
Add frame (dX/dY), add a frame around the dataset by providing vertical and horizontal shifts
Flip horizontally, flip the dataset horizontally
Flip vertically, flip the dataset vertically
Flip Z, flip the Z-stacks of the dataset
Flip T, flip the time vector of the dataset
Rotate 90 degrees, rotate dataset 90 degrees clockwise
Rotate -90 degrees, rotate dataset 90 degrees counterclockwise
Transpose YX -> YZ, transpose the dataset so that YX->YZ
Transpose YX -> XZ, transpose the dataset so that YX->XZ
Transpose YX -> XY, transpose the dataset so that YX->XY
Transpose YX -> ZX, transpose the dataset so that YX->ZX
Transpose Z<->T, transpose the dataset so that Z->T

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Transform - cell string, {Flip horizontally, Flip vertically, Flip Z, Flip T, Rotate 90 degrees, Rotate -90 degrees, Transpose XY -> ZX, Transpose XY -> ZY, Transpose ZX -> ZY, Transpose Z<->T} - available transformation modes
.Position - cell string, {Center, Left-upper corner, Right-upper corner, Left-bottom corner,Right-bottom corner} - position for the add frame modes for Add frame (width/height)
.NewImageWidth - string, width of the image for Add frame (width/height)
.NewImageHeight - string, height of the image for Add frame (width/height)
.FrameColorIntensity - string, intensity if the frame
.FrameWidth - string, width of the frame for Add frame (dX/dY)
.FrameHeight - string, height of the frame for Add frame (dX/dY)
.IntensityPadValue - string, color of the frame for Add frame (dX/dY)
.Method - cell array, {use the pad value, replicate, circular, symmetric} - method for padding for Add frame (dX/dY)
.Direction - cell array, {both, pre, post} - direction of the padding for Add frame (dX/dY)
.showWaitbar - logical, show or not the waitbar

Required fields of BatchOpt:

References mibInputDlg(), mibPath, and handle.notify.

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◆ menuFileChoppedImage_Callback()

function mibController.menuFileChoppedImage_Callback ( parameter )

a callback to Menu->File->Chopped images, chop/rechop dataset to/from smaller subsets

Parameters

parameter

[optional] a string that defines image source:

import, [default] import multiple datasets and assemble them in one big dataset
export, chop the currently opened dataset to a set of smaller ones

◆ menuFileExamples_Callback()

function mibController.menuFileExamples_Callback ( BatchOptIn )

a callback to Menu->File->Example datasets, import an example dataset into MIB

Parameters

BatchOptIn a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables .Dataset -> [cell], dataset name as listed in MIB->Menu->File->Example datasets .DirectoryName -> [cell], output directory only for DeepMIB projects

References mibUpdatePixSizeAndResolution(), handle.notify, handle.permute, handle.reshape, and updateBatchOptCombineFields_Shared().

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◆ menuFileExportImage_Callback()

function mibController.menuFileExportImage_Callback ( parameter )

a callback to Menu->File->Export Image, export image and meta-data from MIB to the main Matlab workspace or Imaris

Parameters

parameter

[optional] a string that defines image source:

matlab, [default] main workspace of Matlab
imaris, to imaris, requires ImarisXT

References handle.disp, mibInputMultiDlg(), and mibSetImarisDataset().

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◆ menuFileImportImage_Callback()

function mibController.menuFileImportImage_Callback ( parameter )

a callback to Menu->File->Import Image, import image from Matlab main workspace or system clipboard

Parameters

parameter

[optional] a string that defines image source:

matlab, [default] main workspace of Matlab
imaris, from imaris, requires ImarisXT
clipboard, from the system clipboard
url, from the provided URL address

References handle.fieldnames, handle.fields, imclipboard(), max, mibGetImarisDataset(), mibInputDlg(), mibInputMultiDlg(), mibPath, handle.notify, handle.reshape, and handle.sort.

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◆ menuFilePreference_Callback()

function mibController.menuFilePreference_Callback ( )

a callback to MIB->Menu->File->Preferences...

◆ menuFileRender_Callback()

function mibController.menuFileRender_Callback ( parameter )

a callback to MIB->Menu->File->Render volume...

%

Note: VolumeViewer is available only for the Matlab version of MIB, requires Matlab R2017a or newer!

Parameters

parameter

a char that specify where to render the volume

fiji - using Fiji 3D viewer
volviewer - using Matlab VolumeViewer application

References max, mibInputMultiDlg(), mibPath, and mibRenderVolumeWithFiji().

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◆ menuFileSaveImageAs_Callback()

function mibController.menuFileSaveImageAs_Callback ( )

a callback to the mibGUI.handles.menuFileSaveImageAs, saves image to a file

◆ menuImageColorCh_Callback()

function mibController.menuImageColorCh_Callback ( parameter )

callback to Menu->Image->Color Channels do actions with individual color channels

Parameters

parameter

a string that defines image source:

Insert empty channel, insert an empty color channel to the specified position
Copy channel, copy color channel to a new position
Invert channel, invert color channel
Rotate channel, rotate color channel
Swap channels, swap two color channels
Delete channel, delete color channel from the dataset

◆ menuImageContrast_Callback()

function mibController.menuImageContrast_Callback ( parameter )

a callback to Menu->Image->Contrast; do contrast enhancement

Parameters

parameter

a string that defines image source:

'CLAHE', contrast adjustment with CLAHE method
'Z stack', normalize layers in the Z-dimension using intensity analysis of complete slices
'Time series', normalize layers in the Time-dimensionusing intensity analysis of complete slices
'Masked area', normalize layers using intensity analysis of complete slices
'Background', normalize layers using intensity analysis of complete slices

BatchOptIn a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event

◆ menuImageIntensity_Callback()

function mibController.menuImageIntensity_Callback ( parameter )

callback to the Menu->Image->Intensity profile; get the image intensity profile

Parameters

parameter

a string that specify the mode of the image intensity profile

line - a linear profile between two points
arbitrary - an arbitrary profile

References handle.findobj, and max.

◆ menuImageInvert_Callback()

function mibController.menuImageInvert_Callback	(		mode,
			BatchOptIn )

callback for Menu->Image->Invert image; start invert image

Parameters

mode

a string that defines part of the dataset to be inverted. When empty BatchOptIn structure will be used or 4D mode

when 2D invert the currently shown slice
when 3D invert the currently shown z-stack
when 4D invert the whole dataset

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.ColorChannels - cell string, ids of color channel, one of these {Shown channels}, {All channels}
.showWaitbar - logical, show or not the waitbar
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuImageMode_Callback()

function status = mibController.menuImageMode_Callback	(		hObject,
			BatchOptIn )

callback to the Menu->Image->Mode, convert image to different formats

Parameters

hObject handle to the selected menu entry

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Target - cell string, {Grayscale, RGB Color, HSV Color, Indexed, 8 bit, 16 bit, 32 bit} - convert dataset to one of these options
.showWaitbar - logical, show or not the waitbar
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

Return values

status

result of the funtion, 1-success, 0-fail | Examples:

// for the batch mode
BatchOptIn.Target = {'Grayscale'};     // define to where convert the dataset
obj.menuImageMode_Callback([], BatchOptIn); // call from mibController class;

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuImageToolsContentAware_Callback()

function mibController.menuImageToolsContentAware_Callback ( )

callback to the Menu->Image->Tools->Content-aware fill, fill the selected area using content aware algorithms

◆ menuImageToolsProjection_Callback()

function mibController.menuImageToolsProjection_Callback ( BatchOptIn )

callback to the Menu->Image->Tools->Intensity projection, calculate intensity projection of the dataset

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details Possible fields,

.ProjectionType - cell string with type of the intensity projection, one of these: {Max, Min, Mean, Median, Sum, Focus stacking}
.Dimension - cell string, with dimension, {Y, X, C, Z, T}
.Destination - cell string with id of the destination container, {Container 1};
.showWaitbar - logical, show or not the waitbar

References fstack_mib(), max, mibInputMultiDlg(), mibPath, min, handle.notify, handle.permute, uint32, and updateBatchOptCombineFields_Shared().

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◆ menuMaskExport_Callback()

function mibController.menuMaskExport_Callback	(		ExportTo,
			BatchOptIn )

callback to Menu->Mask->Export, export the Mask layer to Matlab or another buffer

Parameters

ExportTo

a string that specify the destination, where the mask layer should be exported

Matlab - to the main Matlab workspace
MIB container - another buffer within MIB

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.ExportTo - cell string, {Matlab, MIB container} destination for mask export
.MaskVariable - string, [Matlab export only] name of a variable to be created in the Matlab workspace;
.ContainerId - cell array, {Container d} - index of the container for MIB container mode
.showWaitbar - logical, show or not the waitbar

References handle.disp, mibInputDlg(), mibInputMultiDlg(), mibPath, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuMaskImageReplace_Callback()

function mibController.menuMaskImageReplace_Callback	(		type,
			BatchOptIn )

callback to Menu->Mask->Replace color; Replace image intensities in the Masked or Selected areas with new intensity value

Parameters

type

a string with source layer

mask - replace image intensities under the Mask layer
selection - replace image intensities under the Selection layer

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Target - cell string, {mask, selection} - layer to containing the areas to replace
.ColorIntensity - string,new color intensity for the masked/selected area, one or more numbers from above 0
.showWaitbar - logical, show or not the waitbar
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

References max, mibInputMultiDlg(), mibPath, min, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuMaskImport_Callback()

function mibController.menuMaskImport_Callback	(		ImportFrom,
			BatchOptIn )

callback to Menu->Mask->Import, import the Mask layer from Matlab or another buffer of MIB

ImportFroms

ImportFrom: a string that specify the origin, from where the mask layer should be imported

Matlab - from the main Matlab workspace
MIB container - from another buffer within MIB BatchOptIn: a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables
.ImportFrom - cell string, {Matlab, MIB container} - source of the mask layer to be imported
.MaskVariable - string, [Matlab import only] name of a variable with mask in the Matlab workspace;
.ContainerId - cell array, {Container d} - index of the container for MIB container mode
.showWaitbar - logical, show or not the waitbar

References mibInputMultiDlg(), mibPath, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuMaskInvert_Callback()

function mibController.menuMaskInvert_Callback	(		type,
			BatchOptIn )

callback to Menu->Mask->Invert; invert the Mask/Selection layer

Parameters

type

a string with the layer to invert

mask - invert the Mask layer
selection - invert the Selection layer

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Target - cell string, {mask, selection} - layer to invert
.showWaitbar - logical, show or not the waitbar
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuMaskLoad_Callback()

function mibController.menuMaskLoad_Callback ( )

callback to Menu->Mask->Load Mask; load the Mask layer to MIB from a file

◆ menuMaskSaveAs_Callback()

function mibController.menuMaskSaveAs_Callback ( )

callback to Menu->Mask->Save As; save the Mask layer to a file

◆ menuModelAnn_Callback()

function mibController.menuModelAnn_Callback ( parameter )

callback to Menu->Models->Annotations

Parameters

parameter

a string with parameter

list - show list of annotations
imaris - export annotations to Imaris as spots
delete - % delete all annotations

References max, mibInputMultiDlg(), mibPath, mibSetImarisSpots(), and min.

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◆ menuModelsExport_Callback()

function mibController.menuModelsExport_Callback ( exportTo )

callback to Menu->Models->Export export the Model layer to the main Matlab workspace

Parameters

exportTo

a string with destination for the export

matlab - to Matlab workspace
imaris - to Imaris

◆ menuModelsImport_Callback()

function mibController.menuModelsImport_Callback ( BatchOptIn )

callback to Menu->Models->Import; import the Model layer from the main Matlab workspace

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details

.ModelVariable - string, name of variable when exporting to Matlab workspace
.showWaitbar - logical, show or not the waitbar
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

References max, mibInputMultiDlg(), mibPath, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ menuModelsRender_Callback()

function mibController.menuModelsRender_Callback ( type )

a callback to MIB->Menu->Models->Render model...

Parameters

type

a string with desired rendering engine

'matlab' - Matlab rendering
'matlabImaris' - render model in Matlab and export the rendered
'volviewer' - render model in Matlab Volume Viewer application (only for Matlab version of MIB) surface to Imaris
'fiji' - Fiji rendering
'imaris' - Imaris rendering, i.e. send first a model as a volume and use Imaris to generate the surface

References mibRenderModelImaris().

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◆ menuModelsSaveAs_Callback()

function mibController.menuModelsSaveAs_Callback ( parameter )

callback to Menu->Models->Save as save model to a file

Parameters

parameter

a string

'saveas' -> [default] start a dialog to select saving format and the filename
'save' -> save using existing filename

◆ menuSelectionBuffer_Callback()

function mibController.menuSelectionBuffer_Callback ( parameter )

a callback to Menu->Selection to Buffer... to Copy/Paste/Clear of the selection of the shown layer

Parameters

parameter

a string that defines image source:

'copy', store selection from the current layer to a buffer
'paste', paste selection from the buffer to the current layer
'pasteall', paste selection from the buffer to all Z-layers
'clear', clear selection buffer

References min.

◆ menuSelectionInterpolate()

function mibController.menuSelectionInterpolate ( )

a callback to the Menu->Selection->Interpolate; interpolates shapes of the selection layer

◆ menuSelectionToMaskBorder_Callback()

function mibController.menuSelectionToMaskBorder_Callback ( )

callback to Menu->Selection->Expand to Mask border expand selection to borders of the Masked layer

◆ menuToolsMeasure_Callback()

function mibController.menuToolsMeasure_Callback ( type )

a callback for selection of obj.mibView.handles.menuToolsMeasure entries

Parameters

type	a string with parameter for the tool `tool`, start a measure tool `line`, start a simple line measure tool `freehand`, start a simple freehand measure tool

References handle.disp, and max.

◆ mibAddMaterialBtn_Callback()

function mibController.mibAddMaterialBtn_Callback ( BatchOptIn )

callback to the obj.mibView.handles.mibAddMaterialBtn, add material to the model

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.MaterialName - a string, name of a new material
.showWaitbar - logical, show or not the waitbar

Examples:

obj.mibAddMaterialBtn_Callback(); // add material to the model

References M, max, mibInputDlg(), mibPath, handle.notify, unFocus(), and updateBatchOptCombineFields_Shared().

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◆ mibAnisotropicDiffusion()

function mibController.mibAnisotropicDiffusion	(		filter_type,
			cpuParallelLimit )

Filter image with Anisotropic diffusion filters.

Parameters

filter_type

type of desired filter:

'diplib', use diplib library to do the filtering (http://www.diplib.org/)
'anisodiff', use anisodiff function by Peter Kovesi (http://www.csse.uwa.edu.au/~pk/Research/MatlabFns/#anisodiff)
'coherence_filter', use Image Edge Enhancing Coherence Filter by Dirk-Jan Kroon and Pascal Getreuer (http://www.mathworks.com/matlabcentral/fileexchange/25449-image-edge-enhancing-coherence-filter-toolbox)

cpuParallelLimit max number of CPU available for parallel processing

| strcmp(filter_type,'diplib') % do diplib or anisodiff filtering

References mibDoAndiffFiltering().

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◆ mibAnnMarkerEdit_Callback()

function mibController.mibAnnMarkerEdit_Callback ( )

callback for selection of annotation marker type, updates mibAnnMarkerEdit field of the mibModel

Return values

◆ mibAutoBrightnessBtn_Callback()

function mibController.mibAutoBrightnessBtn_Callback ( )

Adjust brightness automatically for the shown image.

The function stretch the image min and max intensity values to fill the minimal and maximal values of the image container. When handles.brightnessFixCheck == 1 the coefficients are calculated for the whole 3D dataset; when handles.brightnessFixCheck == 0 each single slice adjusted individually.

Return values

References max, mibInputMultiDlg(), and min.

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◆ mibBioformatsCheck_Callback()

function mibController.mibBioformatsCheck_Callback ( )

Bioformats that can be read with loci BioFormats toolbox this function updates the list of file filters in obj.mibView.handles.mibFileFilterPopup.

◆ mibBrushPanelInterpolationSettingsBtn_Callback()

function mibController.mibBrushPanelInterpolationSettingsBtn_Callback ( )

mibBrushPanelInterpolationSettingsBtn_Callback(obj, hObject) callback for modification of superpixel mode settings of the brush tool

References mibInputMultiDlg(), mibPath, and unFocus().

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◆ mibBrushSuperpixelsEdit_Callback()

function mibController.mibBrushSuperpixelsEdit_Callback ( hObject )

mibBrushSuperpixelsEdit_Callback(obj, hObject) callback for modification of superpixel mode settings of the brush tool

Required fields of hObject:

◆ mibBrushSuperpixelsWatershedCheck_Callback()

function mibController.mibBrushSuperpixelsWatershedCheck_Callback ( hObject )

mibBrushSuperpixelsWatershedCheck_Callback(obj, hObject) callback for selection of superpixel mode for the brush tool

Required fields of hObject:

◆ mibBufferToggle_Callback()

function mibController.mibBufferToggle_Callback	(		Id,
			BatchOptIn )

a callback to press of obj.mibView.handles.mibBufferToggle button

Parameters

Id	index of the pressed toggle button
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibBufferToggleContext_Callback()

function mibController.mibBufferToggleContext_Callback	(	parameter,
		buttonID,
		BatchOptIn )

callback function for the popup menu of the buffer buttons in the upper part of the Directory contents panel. This callback is triggered from all those buttons.

Parameters

parameter	- a string that defines options: 'duplicate' - duplicate the dataset to another buffer 'sync_xy' - synchronize datasets with another dataset in XY 'sync_xyz' - synchronize datasets with another dataset in XYZ 'sync_xyzt' - synchronize datasets with another dataset in XYZT 'link_views' - link the view between two containers 'close' - delete the dataset 'closeAll' - delete all datasets
buttonID	- a number (from 1 to 9) of the pressed toggle button.
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

References mibInputMultiDlg(), mibPath, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibChangeLayerEdit_Callback()

function mibController.mibChangeLayerEdit_Callback	(		parameter,
			BatchOptIn )

A callback for changing the slices of the 3D dataset by entering a new slice number.

Parameters

parameter	[optional], when provided: 0 - set dataset to the last slice, used as a callback for mibView.mibLastSliceBtn 1 - set dataset to the first slice, used as a callback for mibView.mibFirstSliceBtn
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event .SliceNumber -> string, slice number to show

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibChangeLayerSlider_Callback()

function mibController.mibChangeLayerSlider_Callback ( )

A callback function for mibGUI.mibChangeLayerSlider. Responsible for showing next or previous slice of the dataset.

References min, and handle.notify.

◆ mibChangeTimeEdit_Callback()

function mibController.mibChangeTimeEdit_Callback	(		parameter,
			BatchOptIn )

A callback for changing the time points of the dataset by entering a new time value.

Parameters

parameter	[optional], when provided: 0 - set dataset to the last slice, used as a callback for mibView.mibLastSliceBtn 1 - set dataset to the first slice, used as a callback for mibView.mibFirstSliceBtn
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event .FrameNumber -> string, frame number to show

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibChangeTimeSlider_Callback()

function mibController.mibChangeTimeSlider_Callback ( )

A callback function for mibGUI.mibChangeTimeSlider. Responsible for showing next or previous time point of the dataset.

References handle.notify.

◆ mibChannelMixerTable_Callback()

function mibController.mibChannelMixerTable_Callback ( type )

a callback for the context menu of obj.mibView.handles.mibChannelMixerTable

Return values

Parameters

type a string with one of the possible options 'Insert empty channel' - insert color channel 'Copy channel' - copy one color channel to another 'Invert channel' - invert color channel 'Rotate channel' - rotate color channel 'Swap channels' - swap two color channels 'Delete channel' - delete color channel 'set color' - set LUT color for the channel

◆ mibChannelMixerTable_CellEditCallback()

function mibController.mibChannelMixerTable_CellEditCallback	(	Indices,
		PreviousData,
		modifier )

a callback edit of a cell in obj.mibView.handles.mibChannelMixerTable

Parameters

Indices	row and column indices of the cell(s) edited
PreviousData	previous data for the cell(s) edited
modifier	a pressed key modifier, [], `control`, `shift`

◆ mibChannelMixerTable_CellSelectionCallback()

function mibController.mibChannelMixerTable_CellSelectionCallback ( Indices )

a callback selection of a cell in obj.mibView.handles.mibChannelMixerTable

Parameters

Indices row and column indices of the cell(s) edited

◆ mibColChannelCombo_Callback()

function mibController.mibColChannelCombo_Callback ( )

callback for modification of obj.View.handles.mibColorChannelCombo box

◆ mibCreateModelBtn_Callback()

function mibController.mibCreateModelBtn_Callback ( )

Create a new model, callback for press of the Create button in mibGUI.

Examples:

mibController.mibCreateModelBtn_Callback(); // create a new model

◆ mibDoUndo()

function mibController.mibDoUndo ( newIndex )

Undo the recent changes with Ctrl+Z shortcut.

Parameters

newIndex [optional] - index of the dataset to restore, when omitted restore the last stored dataset.

References handle.fieldnames, min, handle.notify, and mibImage.viewPort.

◆ mibDragAndDropFiles()

function mibController.mibDragAndDropFiles	(		DragNDrop,
			event )

callback for dropping the files into the image view panel: loading the files

Required fields of event:

References DragNDrop, handle.notify, and handle.sort.

◆ mibDragAndDropModelFiles()

function mibController.mibDragAndDropModelFiles	(		DragNDrop,
			event )

callback for dropping model files into the segmentation table: loading the files

Required fields of event:

References DragNDrop, handle.notify, and handle.sort.

◆ mibEraserEdit_Callback()

function mibController.mibEraserEdit_Callback ( )

increase size of the eraser tool with the provided in obj.mibView.handles.mibEraserEdit

Return values

◆ mibFijiExport()

function mibController.mibFijiExport ( )

Export currently open dataset to Fiji.

Return values

References mibInputDlg(), mibPath, Miji_wrapper(), and handle.permute.

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◆ mibFijiImport()

function mibController.mibFijiImport ( )

import dataset from Fiji to MIB

Return values

References max, mibFijiSelectDataset(), mibPath, Miji_wrapper(), min, handle.notify, handle.permute, handle.reshape, and uint32.

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◆ mibFijiRunMacro()

function mibController.mibFijiRunMacro ( )

run command or macro on Fiji

Return values

References Miji_wrapper().

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◆ mibFileFilterPopup_cm()

function mibController.mibFileFilterPopup_cm ( parameter )

a context menu to the to the handles.mibFileFilterPopup, the menu is called with the right mouse button

Parameters

parameter

a string with parameters for the function

register - register extensions for file filters

References mibInputMultiDlg(), mibPath, and handle.sort.

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◆ mibFilesListbox_Callback()

function mibController.mibFilesListbox_Callback ( )

navigation in the file list, i.e. open file or change directory

References mibLoadImages(), mibPath, handle.notify, and unFocus().

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◆ mibFilesListbox_cm_Callback()

function mibController.mibFilesListbox_cm_Callback	(		parameter,
			BatchOptIn )

a context menu to the to the handles.mibFilesListbox, the menu is called with the right mouse button

Parameters

parameter

a string with parameters for the function

Combine datasets - [default] Combine selected datasets
Load part of dataset - Load part of the dataset
Load each N-th dataset - Load each N-th dataset
Insert into open dataset - Insert into the open dataset
Combine files as color channels - Combine files as color channels
Add as new color channel - Add as a new color channel
Add each N-th dataset as new color channel - Add each N-th dataset as a new color channel
rename - Rename selected file
delete - Delete selected files
file_properties - File properties

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Mode -> [cell], desired mode to combine the images: Combine datasets, Load each N-th dataset, Insert into open dataset, Combine files as color channels, Add as new color channel, Add each N-th dataset as new color channel
.DirectoryName -> [cell] directory name, where the files are located, use the right mouse click over the Parameters table to modify the directory
.FilenameFilter -> [string] filter for filenames: . - process all files in the directory; *.tif - process only the TIF files; could also be a filename
.Filenames -> [A CELL WITHIN CELL ARRAY, optional] with list of FULL PATH filenames to open, only for the batch mode
.UseBioFormats -> [logical] when checked the Bio-Formats reader will be used
.BioFormatsIndices -> [string, BioFormats only] indices of images to be opened for file containers, when empty load all
.EachNthStep -> [string] define step to be used for combining images using each N-th option
.BackgroundColorIntensity -> [string] Intensity of the background color for cases, when width/height of combined images mismatch
.InsertDatasetDimension -> [Insert only, cell] Image dimension to insert the dataset: depth, time
.InsertDatasetPosition -> [Insert only, string] insert position; 1 - beginning of the open dataset; 0 - end of the open dataset\nor type any number to define position
.showWaitbar -> [logical] show or not the waitbar
.id -> [optional], an index dataset from 1 to 9, defalt = currently shown dataset

Required fields of BatchOptIn:

References mibInputDlg(), mibInputMultiDlg(), mibLoadImages(), mibPath, min, handle.notify, unFocus(), and updateBatchOptCombineFields_Shared().

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◆ mibFindMaterialUnderCursor()

function mibController.mibFindMaterialUnderCursor ( )

find material under the mouse cursor, a callback for Ctrl+F key shortcut

References handle.notify.

◆ mibGUI_Brush_scrollWheelFcn()

function mibController.mibGUI_Brush_scrollWheelFcn ( eventdata )

Control callbacks from mouse scroll wheel during the brush tool.

Parameters

eventdata additinal parameters

Required fields of eventdata:

◆ mibGUI_panAxesFcn()

function mibController.mibGUI_panAxesFcn	(	xy,
		imgWidth,
		imgHeight )

This function is responsible for moving image in obj.mibView.handles.mibImageAxes during panning.

Parameters

xy	coordinates of the mouse when the mouse button was pressed
imgWidth	width of the shown image
imgHeight	height of the shown image

◆ mibGUI_PanelShiftBtnUpFcn()

function mibController.mibGUI_PanelShiftBtnUpFcn ( panelName )

callback for the release of a mouse button over handles.mibSeparatingPanel to change size of Directory contents and Segmentation panels

Parameters

panelName

a string with the name of the moved panel

mibSeparatingPanel - for horizontal slider
mibSeparatingPanel2 - for vertical slider

◆ mibGUI_ScrollWheelFcn()

function mibController.mibGUI_ScrollWheelFcn ( eventdata )

Control callbacks from mouse scroll wheel.

This function takes care of the mouse wheel. Depending on a key modifier and

handles.mouseWheelToolbarSw it can

Ctrl+mouse wheel, change size of the brush and some other tools. The value of the new size value is displayed next to the cursor during the mouse wheel rotation.
when handles.mouseWheelToolbarSw is not pressed, the mouse wheel is used for zoom in/zoom out actions.
when handles.mouseWheelToolbarSw is pressed, the mouse wheel is used to change slices of the shown 3D dataset.

Parameters

eventdata additinal parameters

Required fields of eventdata:

References C(), max, and handle.notify.

Referenced by mibMeasure.DistancePolyFun().

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◆ mibGUI_SizeChangedFcn()

function mibController.mibGUI_SizeChangedFcn ( resizeParameters )

resizing for panels of MIB

Parameters

resizeParameters an optional structure used when move vertical (mibView.handles.mibSeparatingPanel) and horizontal (mibView.handles.mibSeparatingPanel2) resize panel sliders .name - a string with name of the panel .panelShift - a number with shift of the panel or true/false state to show or hide the top and bottom panels

Required fields of resizeParameters:

References max.

◆ mibGUI_WindowBrushMotionFcn()

function mibController.mibGUI_WindowBrushMotionFcn	(	selection_layer,
		structElement,
		currMask )

This function draws the brush trace during use of the brush tool.

Parameters

selection_layer	when 'mask' limit selection to the masked area, could be ''
structElement	a structural element to be used with the brush, similar to the one generated with Matlab strel function
currMask	is a bitmap with the Mask image, needed for selection_layer == 'mask'

References min.

◆ mibGUI_WindowButtonDownFcn()

function mibController.mibGUI_WindowButtonDownFcn ( )

this is callback for the press of a mouse button

References handle.findobj, max, and min.

◆ mibGUI_WindowButtonUpDragAndDropFcn()

function mibController.mibGUI_WindowButtonUpDragAndDropFcn	(	mode,
		diffX,
		diffY,
		BatchOptIn )

callback for release of the mouse button after use of the Drag and Drop materials tool

Parameters

mode	- mode for the drag and drop action - '2D, Slice', drag all selection shown on the current slice - 'Object2D', drag the selected object only on the current slice - '3D, Stack', drag all selection for all slices of the dataset - 'Object3D', drag the selected 3D object
diffX	- [optional] optional value for shift in dX direction, not compatible with the 'Object2D' mode
diffY	- [optional] optional value for shift in dY direction, not compatible with the 'Object2D' mode
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables .Target = 'Layer to be moved .Mode = 'Part of the dataset to be moved .shiftX = 'X-shift in pixels .shiftY = 'Y-shift in pixels .showWaitbar = 'Show or not the progress bar during execution

References handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibGUI_WindowButtonUpFcn()

function mibController.mibGUI_WindowButtonUpFcn ( brush_switch )

callback for release of the mouse button

Parameters

brush_switch when 'subtract' - subtracts the brush selection from the existing selection, needed for return after the brush drawing tool

References mibPath.

◆ mibGUI_WindowDragAndDropMotionFcn()

function mibController.mibGUI_WindowDragAndDropMotionFcn ( selection_layer )

This function draws the displaced materials during use of the drag and drop materials tool.

Parameters

brushSelection an image of the selected layer

◆ mibGUI_WindowKeyPressFcn()

function mibController.mibGUI_WindowKeyPressFcn	(		hObject,
			eventdata )

callback for a key press in mibGUI

Parameters

hObject	handle of the focused object
eventdata	structure with the following fields (see FIGURE) Key -> name of the key that was released, in lower case Character -> character interpretation of the key(s) that was released Modifier -> name(s) of the modifier key(s) (i.e., control, shift) released

Required fields of hObject:

Required fields of eventdata:

| x < 1 || x > handles.Img{handles.Id}.I.no_stacks;

References handle.isvalid, max, and handle.notify.

◆ mibGUI_WindowKeyPressFcn_BrushSuperpixel()

function mibController.mibGUI_WindowKeyPressFcn_BrushSuperpixel ( eventdata )

a function to check key callbacks when using the Brush in the Superpixel mode

Parameters

eventdata structure with the following fields (see FIGURE) Key -> name of the key that was released, in lower case Character -> character interpretation of the key(s) that was released Modifier -> name(s) of the modifier key(s) (i.e., control, shift) released

Required fields of eventdata:

◆ mibGUI_WindowKeyReleaseFcn()

function mibController.mibGUI_WindowKeyReleaseFcn ( eventdata )

callback for release of keys in mibGUI window

Parameters

eventdata structure with the following fields (see FIGURE) Key -> name of the key that was released, in lower case Character -> character interpretation of the key(s) that was released Modifier -> name(s) of the modifier key(s) (i.e., control, shift) released

References max.

◆ mibGUI_WinMouseMotionFcn()

function mibController.mibGUI_WinMouseMotionFcn ( )

returns coordinates and image intensities under the mouse cursor

References min.

◆ mibImageFilterDoitBtn_Callback()

function mibController.mibImageFilterDoitBtn_Callback ( )

a callback to the obj.mibView.handles.mibImageFilterDoitBtn, apply image filtering using the selected filter

References mibDoImageFiltering(), and n.

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◆ mibLoadModelBtn_Callback()

function mibController.mibLoadModelBtn_Callback ( )

callback to the obj.mibView.handles.mibLoadModelBtn, loads model to MIB from a file

Examples:

obj.mibLoadModelBtn_Callback(); // call from mibController; load a model

◆ mibLutCheckbox_Callback()

function mibController.mibLutCheckbox_Callback ( )

a callback to the mibGUI.handles.mibLutCheckbox, turn on/off visualization of color channels using luck-up table (LUT)

References unFocus().

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◆ mibMaskedAreaCheck_Callback()

function mibController.mibMaskedAreaCheck_Callback ( )

a callback to the mibGUI.handles.mibMaskedAreaCheck, allows to toggle state of the Masked area

References unFocus().

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◆ mibMaskGenerator()

function mibController.mibMaskGenerator ( type )

generate the Mask later

Parameters

type	a type of the mask generator: 'new' - generate a new mask 'add' - generate mask and add it to the existing mask

References mibGetFrangiMask(), mibGetMorphMask(), mibGetStrelMask(), and handle.permute.

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◆ mibMaskRecalcStatsBtn_Callback()

function mibController.mibMaskRecalcStatsBtn_Callback ( )

recalculate objects for Mask or Model layer to use with the Object Picker tool in 3D

This function populates mibModel.maskStat structure

◆ mibMaskShowCheck_Callback()

function mibController.mibMaskShowCheck_Callback ( )

a callback to the mibGUI.handles.maskShowCheck, allows to toggle visualization of the mask layer

References unFocus().

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◆ mibModelPropertyUpdate()

function mibController.mibModelPropertyUpdate ( parameter )

% update switches in the obj.mibModel class that describe states of GUI widgets

Parameters: a string with the parameter name

mibHideImageCheck - enable or disable visualization of the Image layer
mibLiveStretchCheck - enable or diable the live stretching of image intensities
mibModelTransparencySlider - transparency value for the model layer
mibMaskTransparencySlider - transparency value for the mask layer
mibSelectionTransparencySlider - transparency value for the selection layer
mibSegmShowTypePopup - type of model visualization: 1 - filled; 2 - contour
mibAnnValueEccentricCheck - enable value-eccentric annotations

Return values

◆ mibModelShowCheck_Callback()

function mibController.mibModelShowCheck_Callback ( )

callback to the mibGUI.handles.mibModelShowCheck to toggle the Model layer on/off

Return values

◆ mibPixelInfo_Callback()

function mibController.mibPixelInfo_Callback	(		parameter,
			BatchOptIn )

center image to defined position it is a callback from a popup menu above the pixel information field of the Path panel

Parameters

parameter	- a string that defines options: 'jump' - center the viewing window around specified coordinates
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event .x -> string, x-coordinate, when missing or empty the view is not moved in this direction .y -> string, x-coordinate, when missing or empty the view is not moved in this direction .z -> string, x-coordinate, when missing or empty the view is not moved in this direction

References mibInputMultiDlg(), handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibRecolorLabels()

function mibController.mibRecolorLabels ( )

recolor color map for 65535+ models

◆ mibRemoveMaterialBtn_Callback()

function mibController.mibRemoveMaterialBtn_Callback ( BatchOptIn )

callback to the obj.mibView.handles.mibRemoveMaterialBtn, remove material from the model

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.MaterialIndices - a string, indices of materials to be removed
.showWaitbar - logical, show or not the waitbar

Examples:

obj.mibRemoveMaterialBtn_Callback(); // add material to the model

References mibInputMultiDlg(), mibPath, handle.notify, handle.reshape, handle.sort, unFocus(), and updateBatchOptCombineFields_Shared().

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◆ mibRoiAddBtn_Callback()

function mibController.mibRoiAddBtn_Callback ( )

a callback to handles.mibRoiAddBtn, adds a roi to a dataset

◆ mibRoiList_cm_Callback()

function mibController.mibRoiList_cm_Callback ( parameter )

a callback for obj.mibView.handles.mibRoiList context menu

Parameters

parameter

a string with selected action

- 'rename' - rename ROI
- 'edit' - modify ROI
- 'remove' - remove ROI

References mibInputDlg(), mibPath, handle.notify, and unFocus().

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◆ mibRoiLoadBtn_Callback()

function mibController.mibRoiLoadBtn_Callback ( )

a callback to the obj.mibView.handles.mibRoiLoadBtn, loads roi from a file to MIB

References mib_uigetfile().

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◆ mibRoiOptionsBtn_Callback()

function mibController.mibRoiOptionsBtn_Callback ( parameter )

update ROI visualization settings, as callback of mibGUI.handles.mibRoiOptionsBtn

◆ mibRoiRemoveBtn_Callback()

function mibController.mibRoiRemoveBtn_Callback ( )

a callback to obj.mibView.handles.mibRoiRemoveBtn, remore selected ROI

◆ mibRoiSaveBtn_Callback()

function mibController.mibRoiSaveBtn_Callback ( )

a callback to the obj.mibView.handles.mibRoiSaveBtn, saves roi to a file in the matlab format

◆ mibRoiShowCheck_Callback()

function mibController.mibRoiShowCheck_Callback ( parameter )

toggle show/hide state of ROIs, as callback of mibGUI.handles.mibRoiShowCheck

Parameters

parameter a string: when noplot do not redraw the image (used from updateGuiWidgets function)

◆ mibRoiToSelectionBtn_Callback()

function mibController.mibRoiToSelectionBtn_Callback ( )

a callback to obj.mibView.handles.mibRoiToSelectionBtn, highlight area under the selected ROI in the Selection layer

◆ mibSegmAnnDeleteAllBtn_Callback()

function mibController.mibSegmAnnDeleteAllBtn_Callback ( )

callback to Menu->Models->Annotations...->Delete all annotations, delete all annotations of the model

References handle.notify.

◆ mibSegmentation3dBall()

function mibController.mibSegmentation3dBall	(	y,
		x,
		z,
		modifier,
		BatchOptIn )

Do segmentation using the 3D ball tool.

Parameters

y	y-coordinate of the 3D ball center
x	x-coordinate of the 3D ball center
z	z-coordinate of the 3D ball center
modifier	a string, to specify what to do with the generated selection empty - add to 3D ball to the selection layer 'control' - remove 3D ball from the selection layer
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables .Radius - Spot radius in pixels .X - Vector or a single X coordinate of the spot center .Y - Vector or a single X coordinate of the spot center .Z - Vector or a single Z coordinate of the spot center, keep empty to use the currently shown .Mode - Add or subtract spot at the provided coordinate(s) .FixSelectionToMask - Apply thresholding only to the masked area .FixSelectionToMaterial - Apply thresholding only to the area of the selected material; use Modify checkboxes to update the selected material .Target - Destination layer for spot .showWaitbar - Show or not the progress bar during execution

Examples:

obj.mibSegmentation3dBall(50, 75, 10, ''); // call from mibController; add a 3D ball to position [y,x,z]=50,75,10

References max, min, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibSegmentationAnnotation()

function mibController.mibSegmentationAnnotation	(	y,
		x,
		z,
		t,
		modifier,
		options )

Add text annotation to the dataset.

Parameters

y	y-coordinate of the annotation point
x	x-coordinate of the annotation point
z	z-coordinate of the annotation point
t	t-coordinate of the annotation point
modifier	a string, to specify what to do with the generated selection empty - add annotation to the list of annotations (obj.mibModel.I{obj.mibModel.Id}.hLabels as called from mibController) 'control' - remove closest annotation from the annotation list
options	[Optional] structure with additional settings .samInteractiveModel - logical, indicating that the tool is used to perform segmentation using segment-anything model Return values:

Required fields of options:

Examples:

obj.mibSegmentationAnnotation(50, 75, 10, 1, ''); // add an annotation to position [y,x,z,t]=50,75,10,1

References mibInputMultiDlg(), mibPath, min, and handle.notify.

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◆ mibSegmentationBlackWhiteThreshold()

function mibController.mibSegmentationBlackWhiteThreshold	(		parameter,
			BatchOptIn )

Perform black and white thresholding for BW Threshold tool of the 'Segmentation panel'.

Parameters

parameter

a tag of the calling object

'mibSegmLowEdit' - callback after enter a new value to the obj.mibView.handles.mibSegmLowEdit editbox
'mibSegmHighEdit' - callback after enter a new value to the obj.mibView.handles.mibSegmHighEdit editbox
'mibSegmLowSlider' - callback after interacting with the obj.mibView.handles.mibSegmLowSlider slider
'mibSegmHighSlider' - callback after interacting with the obj.mibView.handles.mibSegmHighSlider slider
'mibSegmThresPanelThreshold' - callback after press of the Threshold button

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Mode - Apply thresholding for the current slice (2D), current stack (3D) or the whole dataset(4D)
.MinValue - Minimum intensity or Sensitivity value for thresholding
.MaxValue - Maximum intensity or Width value for thresholding
.ColorChannel - Color channel to be used for thresholding
.FixSelectionToMask - Apply thresholding only to the masked area
.FixSelectionToMaterial - Apply thresholding only to the area of the selected material; use Modify checkboxes to update the selected material
.Adaptive - Enable the adaptive thresholding; use MinValue to specifty Sensitivity and MaxValue to specify Width
.AdaptiveInvert - Adaptive only] invert dataset before adaptive thresholding
.AdaptiveForegroundPolarity - [Adaptive only] determine which pixels are considered foreground pixels
.Target - Destination layer for the thresholding
.showWaitbar - Show or not the progress bar during execution Return values:

References max, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibSegmentationBrush()

function mibController.mibSegmentationBrush	(	y,
		x,
		modifier )

mibSegmentation_Brush(obj, y, x, modifier) Do segmentation using the brush tool

Parameters

y	y-coordinate of the mouse cursor at the starting point
x	x-coordinate of the mouse cursor at the starting point
modifier	a string, to specify what to do with the generated selection empty - add selection 'control' - remove selection from the existing one

Examples:

obj.mibSegmentation_Brush(50, 75, ''); // start the brush tool from position [y,x]=50,75,10

References drawregionboundaries(), max, and min.

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◆ mibSegmentationDragAndDrop()

function mibController.mibSegmentationDragAndDrop	(	y,
		x,
		modifier )

mibSegmentationDragAndDrop(y, x, modifier) Fix segmentation or mask/selection layers by dragging individual 2D/3D objects or complete models with a mouse

Parameters

y	y-coordinate of the mouse cursor at the starting point
x	x-coordinate of the mouse cursor at the starting point
modifier	a string, to specify what to do with the generated selection 'shift' - shift all object on the slice 'control' - shift only a single selected object Return values:

Examples:

obj.mibSegmentationDragAndDrop(50, 75, 'control'); // start the drag and drop tool from position [y,x]=50,75,10

References handle.notify.

◆ mibSegmentationLasso()

function mibController.mibSegmentationLasso ( modifier )

Do segmentation using the lasso tool.

Parameters

modifier

a string, to specify what to do with the generated selection

empty - makes new selection
'control' - removes selection from the existing one

References max, and handle.notify.

◆ mibSegmentationLassoManual()

function mibController.mibSegmentationLassoManual ( modifier )

Do manual segmentation using the lasso tool in the manual mode.

use the following fields to define selected area: obj.mibView.handles.mibSegmObjectPickerPanelSub2X1, obj.mibView.handles.mibSegmObjectPickerPanelSub2Y1, obj.mibView.handles.mibSegmObjectPickerPanelSub2Width, obj.mibView.handles.mibSegmObjectPickerPanelSub2Height edit boxes

Parameters

modifier

a string, to specify what to do with the generated selection

empty - makes new selection
'control' - removes selection from the existing one

◆ mibSegmentationLines3D()

function mibController.mibSegmentationLines3D	(	y,
		x,
		z,
		modifier )

output = mibSegmentationLines3D(obj, y, x, z, modifier) Add and modify 3D lines

Parameters

y	y-coordinate of the node
x	x-coordinate of the node
z	z-coordinate of the node
modifier	a string, to specify what to do with the next point empty - add as a new node to the existing tree 'shift' - defines as the first node of a new tree

References handle.notify.

◆ mibSegmentationMagicWand()

function mibController.mibSegmentationMagicWand	(		yxzCoordinate,
			modifier )

Do segmentation using the Magic Wand tool.

Parameters

yxzCoordinate	a vector with [y,x,z] coodrinates of the starting point, for 2d case it is enough to have only [y, x].
modifier	a string, to specify what to do with the generated selection empty - makes new selection 'shift' - add selection to the existing one 'control' - removes selection from the existing one

Examples:

yxzCoordinate = [50, 75];

obj.mibSegmentationMagicWand(yxzCoordinate, modifier); // call from mibController; start the magic wand tool from position [y,x]=50,75

References min, and handle.notify.

◆ mibSegmentationMembraneClickTraker()

function output = mibController.mibSegmentationMembraneClickTraker	(	yxzCoordinate,
		yx,
		modifier )

output = mibSegmentationMembraneClickTraker(obj, yxzCoordinate, yx, modifier) Trace membranes and draw a straight lines in 2d and 3d

Parameters

yxzCoordinate	a vector with [y,x,z] coodrinates of the starting point (match voxel coordinates of the dataset)
yx	a vector [y,x] with coordinates of the clicked point
modifier	a string, to specify what to do with the generated selection empty - trace membrane from the starting to the selected point 'shift' - defines the starting point of a membrane

Return values

output

a string that defines what next to do in the im_browser_WindowButtonDown function

'continue' - continue with the script
'return' - stop execution and return

References max, mibConnectPoints(), mibTraceCurve(), min, and handle.notify.

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◆ mibSegmentationObjectPicker()

function mibController.mibSegmentationObjectPicker	(		yxzCoordinate,
			modifier )

Select 2d/3d objects from the Mask or Model layers.

Parameters

yxzCoordinate	a vector with [y,x,z] coodrinates of the starting point, for 2d case it is enough to have only [y, x].
modifier	a string, to specify what to do with the generated selection empty - makes new selection 'control' - removes selection from the existing one

Examples:

yxzCoordinate = [50, 75];

handles = obj.mibSegmentationObjectPicker(yxzCoordinate, modifier); // call from mibController; select object at position [y,x]=50,75

References max, and handle.notify.

◆ mibSegmentationPanelCheckboxes()

function mibController.mibSegmentationPanelCheckboxes ( BatchOptIn )

a function of the batch mode that allow to tweak the status of checkboxes of the Segmentation panel

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.FixSelectionToMaterial - a cell, fix selection to material, modifies mibSegmSelectedOnlyCheck
.MaskedArea - a cell, fix selection to the masked area, modifies mibMaskedAreaCheck
.BrushWatershed - a cell, use brush with watershed clustering, modifies mibBrushSuperpixelsWatershedCheck
.BrushSlic - a cell, use brush with slic clustering, modifies mibBrushSuperpixelsCheck
.SelectedMaterial - string, index of the selected material, -1 for mask, 0-for exterior, 1,2..-indices of materials
.selectedAddToMaterial - string, index of the selected add to material, -1 for mask, 0-for exterior, 1,2..-indices of materials

Examples:

BatchOptIn.FixSelectionToMaterial = {'Checked'};

obj.segmentationPanelCheckboxes_Callback(BatchOptIn); // check the Fix Selection To Material checkbox

References handle.fieldnames, handle.notify, state, and updateBatchOptCombineFields_Shared().

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◆ mibSegmentationRegionGrowing()

function mibController.mibSegmentationRegionGrowing	(		yxzCoordinate,
			modifier )

Do segmentation using the Region Growing method.

Based on Fast 3D/2D Region Growing (MEX), written by Christian Wuerslin, Stanford University. http://www.mathworks.com/matlabcentral/fileexchange/41666-fast-3d-2d-region-growing–mex- Requires: compiled RegionGrowing_mex.cpp To compile: "mex RegionGrowing_mex.cpp"

Parameters

yxzCoordinate	a vector with [y,x,z] coodrinates of the starting point, for 2d case it is enough to have only [y, x].
modifier	a string, to specify what to do with the generated selection empty - makes new selection 'shift' - add selection to the existing one 'control' - removes selection from the existing one

Examples:

yxzCoordinate = [50, 75];

obj.mibSegmentationRegionGrowing(yxzCoordinate, modifier); // call from mibController; start the region growing segmentation tool from position [y,x]=50,75

References dMaxDif, and min.

◆ mibSegmentationSAM()

function mibController.mibSegmentationSAM	(		extraOptions,
			BatchOptIn )

Perform segmentation using segment-anything model https://segment-anything.com.

Parameters

extraOptions

structure with additional options

.addNextMaterial, [logical], switch to add next material for the "add, +next material" mode

BatchOptIn

structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Method - Specify method how SAM should be executed -> "Interactive", by interactively adding point -> "Landmarks", process the placed points all at once -> "Automatic everything", automatically segment all objects on the image
.Dataset - segment the current slice (2D, Slice), current stack (3D, Stack) or the whole dataset(4D, Dataset)
.Destination - string with MIB layer to apply results of the segmentation (selection, mask, model)
.showWaitbar - Show or not the progress bar during execution Return values:

Required fields of extraOptions:

References max, min, handle.notify, showErrorDialog(), and updateBatchOptCombineFields_Shared().

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◆ mibSegmentationSAM2()

function mibController.mibSegmentationSAM2	(		extraOptions,
			BatchOptIn )

Perform segmentation using segment-anything-2 model https://github.com/facebookresearch/segment-anything-2.

Parameters

extraOptions

structure with additional options

.addNextMaterial, [logical], switch to add next material for the "add, +next material" mode

BatchOptIn

structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Method - Specify method how SAM should be executed -> "Interactive", by interactively adding point -> "Landmarks", process the placed points all at once -> "Automatic everything", automatically segment all objects on the image
.Dataset - segment the current slice (2D, Slice), current stack (3D, Stack) or the whole dataset(4D, Dataset)
.Destination - string with MIB layer to apply results of the segmentation (selection, mask, model)
.showWaitbar - Show or not the progress bar during execution Return values:

Required fields of extraOptions:

References max, min, handle.notify, handle.permute, showErrorDialog(), and updateBatchOptCombineFields_Shared().

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◆ mibSegmentationSAM_requirements()

function status = mibController.mibSegmentationSAM_requirements ( samVersion )

Check for files required to run segmentation using segment-anything model https://segment-anything.com.

Parameters

samVersion	integer with version of SAM 1 -> default, the first version SAM (https://segment-anything.com) 2 -> the second version SAM-2 (https://github.com/facebookresearch/segment-anything-2) Return values:
status	[logical], switch indicating success of the function

◆ mibSegmentationSpot()

function mibController.mibSegmentationSpot	(	y,
		x,
		modifier,
		BatchOptIn )

mibSegmentationSpot(obj, y, x, modifier, BatchOptIn) Do segmentation using the spot tool

Parameters

y	y-coordinate of the spot center
x	x-coordinate of the spot center
modifier	a string, to specify what to do with the generated selection empty - makes new selection 'control' - removes selection from the existing one
BatchOptIn	a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables .Shape - shape of the spot "circle"/"square" .Radius - Spot radius in pixels, or 2 numbers to set it to half width/height .X - Vector or a single X coordinate of the spot center .Y - Vector or a single X coordinate of the spot center .Z - Vector or a single Z coordinate of the spot center, keep empty to use the currently shown .Mode - Add or subtract spot at the provided coordinate(s) .Check3D - Make spot in 3D, the spot will be shown on all slices .FixSelectionToMask - Apply thresholding only to the masked area .FixSelectionToMaterial - Apply thresholding only to the area of the selected material; use Modify checkboxes to update the selected material .Orientation - Orientation of the dataset .Target - Destination layer for spot .showWaitbar - Show or not the progress bar during execution

References min, handle.notify, and updateBatchOptCombineFields_Shared().

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◆ mibSegmentationTable_CellSelectionCallback()

function mibController.mibSegmentationTable_CellSelectionCallback ( eventdata )

mibSegmentationTable_CellSelectionCallback(obj, eventdata) Callback for cell selection in the handles.mibSegmentationTable table of mibGIU.m

Required fields of eventdata:

◆ mibSegmentationTable_cm_Callback()

function mibController.mibSegmentationTable_cm_Callback	(		hObject,
			type )

a callback to the context menu of mibView.handles.mibSegmentationTable

Parameters

hObject handle of the selected menu entry

type

a string with parameters for the function

'showselected' - toggle display of selected/all materials
'rename' - Rename material
'set color' - Set color of the selected material
'statistics' - Get statistics for material
'mib' - render as volume, R2018b and newer
'isosurface' - Show isosurface (Matlab)
'isosurface2imaris' - render isosurface in Matlab and export to Imaris
'volumeFiji' - Show as volume (Fiji)

References max, mibInputMultiDlg(), mibPath, mibRenderModel(), and mibRenderModelFiji().

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◆ mibSegmentationToolPopup_Callback()

function mibController.mibSegmentationToolPopup_Callback ( )

a callback to the handles.mibSegmentationToolPopup, allows to select tool for the segmentation

◆ mibSegmFavToolCheck_Callback()

function mibController.mibSegmFavToolCheck_Callback ( )

callback to the obj.mibView.handles.mibSegmFavToolCheck, to add the selected tool to the list of favourites

References handle.sort.

◆ mibSegmSAMPanel_Callbacks()

function mibController.mibSegmSAMPanel_Callbacks ( tag )

callbacks for widgets of obj.mibView.handles.mibSegmSAMPanel

Parameters

tag	handle to a widget that has been modified

References mibInputMultiDlg(), mibPath, and unFocus().

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◆ mibSegmSelectedOnlyCheck_Callback()

function mibController.mibSegmSelectedOnlyCheck_Callback ( )

a callback to the mibGUI.handles.mibSegmSelectedOnlyCheck, allows to toggle state of the Fix selection to material

References unFocus().

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◆ mibSelectionButton_Callback()

function mibController.mibSelectionButton_Callback ( action )

a callback to A, S, R buttons in the Selection panel of obj.mibView.gui

Parameters

action

a string that defines type of the action:

when add add selection to the active material of the model or to the Mask layer
when subtract subtract selection from the active material of the model or from the Mask layer
when replace replace the active material of the model or the Mask layer with selection

◆ mibSelectionClearBtn_Callback()

function mibController.mibSelectionClearBtn_Callback ( )

a callback to the mibGUI.handles.mibSelectionClearBtn, allows to clear the Selection layer

◆ mibSelectionDilateBtn_Callback()

function mibController.mibSelectionDilateBtn_Callback ( )

a callback to the mibGUI.handles.mibSelectionDilateBtn, expands the selection layer

◆ mibSelectionErodeBtn_Callback()

function mibController.mibSelectionErodeBtn_Callback ( )

a callback to the mibGUI.handles.mibSelectionErodeBtn, shrinks the selection layer

◆ mibSelectionFillBtn_Callback()

function mibController.mibSelectionFillBtn_Callback ( )

a callback to the mibGUI.handles.mibSelectionFillBtn, allows to fill holes for the Selection layer

◆ mibSelectionPanelCheckboxes()

function mibController.mibSelectionPanelCheckboxes ( BatchOptIn )

a function of the batch mode that allow to tweak the status of checkboxes of the Selection panel

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.Checkbox3D - cell, modify the status of mibActions3dCheck
.ColorChannel - string, empty - do not modify; otherwise index of the color channel to set 0 - All, 1 - first, 2 - second, etc

Examples:

BatchOptIn.Checkbox3D = {'Checked'};

obj.mibSelectionPanelCheckboxes(BatchOptIn); // check the 3D checkbox, call from mibController

References handle.fieldnames, max, min, handle.notify, state, and updateBatchOptCombineFields_Shared().

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◆ mibShowMilestoneDialog()

function mibController.mibShowMilestoneDialog ( mode )

show a milestone dialog with user performance and stats

Return values

Parameters

mode	[string], optional, when `currentStats` - show the current stats `milestoneReached` - show congratulations with the milestone reach (default)

References mibInputMultiDlg(), mibPath, and min.

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◆ mibToolbar_ZoomBtn_ClickedCallback()

function mibController.mibToolbar_ZoomBtn_ClickedCallback	(		hObject,
			recenterSwitch )

modifies magnification using the zoom buttons in the toolbar of MIB

Parameters

hObject	a string with tag of the pressed button
recenterSwitch	[optional], defines whether the image should be recentered after zoom/unzoom. Default=0

◆ mibToolbarPlaneToggle()

function mibController.mibToolbarPlaneToggle	(		hObject,
			moveMouseSw )

a callback to the change orientation buttons in the toolbar of MIB; it toggles viewing plane: xy, zx, or zy direction

Parameters

hObject	handle to im_browser.m (see GCBO)
moveMouseSw	[optional] -> when 1, moves the mouse to the point where the the plane orientation has been changed

Required fields of hObject:

References makeViewMatrix().

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◆ mibUpdatePresetFromSegmentationSettings()

function mibController.mibUpdatePresetFromSegmentationSettings ( presetId )

update preset using the current settings of the selected segmentation tool; this function is a callback on press of Shift+1, Shift+2, Shift+3 default key shortcuts

See also: mibUpdateSegmentationSettingsFromPreset.m

Parameters

presetId a number from 1 to 3 specifying the required preset to use

◆ mibUpdateSegmentationSettingsFromPreset()

function mibController.mibUpdateSegmentationSettingsFromPreset ( presetId )

update settings of the selected segmentation tool from preset, this function is a callback on press of 1,2,3 default key shortcuts

See also: mibUpdatePresetFromSegmentationSettings.m

Parameters

presetId a number from 1 to 3 specifying the required preset to use

◆ mibViewSettingsPanelCheckboxes()

function mibController.mibViewSettingsPanelCheckboxes ( BatchOptIn )

a function of the batch mode that allow to tweak status of checkboxes of the View Settings panel

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event, see Declaration of the BatchOpt structure below for details, the function variables are preferred over the BatchOptIn variables

.FixSelectionToMaterial - a cell, fix selection to material, modifies mibSegmSelectedOnlyCheck
.MaskedArea - a cell, fix selection to the masked area, modifies mibMaskedAreaCheck
.BrushWatershed - a cell, use brush with watershed clustering, modifies mibBrushSuperpixelsWatershedCheck
.BrushSlic - a cell, use brush with slic clustering, modifies mibBrushSuperpixelsCheck
.SelectedMaterial - string, index of the selected material, -1 for mask, 0-for exterior, 1,2..-indices of materials
.selectedAddToMaterial - string, index of the selected add to material, -1 for mask, 0-for exterior, 1,2..-indices of materials

Examples:

BatchOptIn.LUT = {'Checked'};

obj.mibViewSettingsPanelCheckboxes(BatchOptIn); // check the Fix Selection To Material checkbox

References handle.fieldnames, handle.notify, state, and updateBatchOptCombineFields_Shared().

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◆ mibZoomEdit_Callback()

function mibController.mibZoomEdit_Callback ( BatchOptIn )

callback function for modification of the handles.mibZoomEdit

Parameters

BatchOptIn

a structure for batch processing mode, when NaN return a structure with default options via "syncBatch" event

.Mode -> cell, magnification mode: Fit to screen, 100%, Zoom in, Zoom out, Set magnification
.MagnificationValue -> string, new magnification value

References handle.notify, unFocus(), and updateBatchOptCombineFields_Shared().

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◆ plotImage()

function mibController.plotImage	(		resize,
			sImgIn )

Plot image to mibImageAxes. The main drawing function.

Parameters

resize	[optional] when 0 [default] keep the current vieweing settings when 1 resize image to fit the screen
sImgIn	a custom 2D image to show in the axes that should be targeted to the axes. Use resize=0 to show `sImgIn` in the same scale/position as the currently shown dataset, or resize=1 to show `sImgIn` in full resolution

Return values

handles - handles of im_browser.m

Examples:

obj.plotImage(1); // call from mibController: plot image resize it

References handle.findobj, handle.isvalid, and min.

Referenced by mibMeasure.AngleFun(), mibMeasure.CaliperFun(), mibMeasure.CircleFun(), mibMeasure.DistanceFreeFun(), mibMeasure.DistanceFun(), mibMeasure.DistancePolyFun(), mibRoiRegion.imellipseFun(), mibRoiRegion.impolyFun(), mibRoiRegion.imrectFun(), and mibMeasure.PointFun().

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◆ purgeControllers()

static function mibController.purgeControllers	(	obj,
		src,
		evnt )

static

> Description of events find index of the child controller

Required fields of obj:

◆ redrawMibChannelMixerTable()

function mibController.redrawMibChannelMixerTable ( )

Update obj.mibView.handles.mibChannelMixerTable table and obj.mibView.handles.mibColChannelCombo color combo box.

◆ setMeta()

function mibController.setMeta ( meta )

set meta data for the currently shown dataset, mibImage.meta

Parameters

meta	information about the dataset, an instance of the `containers`.`Map` class

Examples:

obj.getMeta(meta); // Call from mibController: update meta information for the currently shown dataset

◆ startController()

function mibController.startController	(		controllerName,
			varargin )

start a child controller using provided name

Parameters

controllerName a string with name of a child controller, for example, mibImageAdjController

varargin

additional optional controllers or parameters

startController ( ..., varargin{2} )

mibController.startController

function startController(controllerName, varargin)

start a child controller using provided name

Definition startController.m:18

varargin

A variable number of input arguments.

Required Parameters for varargin:

varargin{2} a structure with parameters for the batch processing, see mibHistThresController. names of the fields can be seen in the alt-text of the widgets!

Examples:

handles.mibController.startController('mibImageAdjController'); // start a child controller from a callback for handles.mibDisplayBtn press

BatchOpt.colChannel = 1;    % color channel for thresholding
BatchOpt.Mode = '3D, Stack';     % mode to use
BatchOpt.Method = 'Otsu';       % thresholding algorithm
BatchOpt.t = [1 1];     % [optional] time points, [t1, t2]
BatchOpt.z = [1 10];    % [optional] slices, [z1, z2]
BatchOpt.x = [10 120];    % [optional] slices, [x1, x2]
BatchOpt.Orientation = 2; % [optional] dataset orientation
obj.startController('mibHistThresController', [], BatchOpt);

References handle.addlistener, handle.fieldnames, mibController(), and handle.notify.

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◆ startPlugin()

function mibController.startPlugin ( pluginName )

start plugin from MIB menu

Return values

Parameters

pluginName name of the plugin (same as name of directory where it is stored)

◆ toolbarBlockModeSwitch_ClickedCallback()

function mibController.toolbarBlockModeSwitch_ClickedCallback ( )

a callback for press of obj.mibView.toolbarBlockModeSwitch in the toolbar of MIB

◆ toolbarCenterPointShow_ClickedCallback()

function mibController.toolbarCenterPointShow_ClickedCallback ( )

a callback for press of obj.mibView.toolbarCenterPointShow in the toolbar of MIB. Toggles display of a center point over the mibImageAxis

References handle.isvalid, and mibPath.

◆ toolbarInterpolation_ClickedCallback()

function mibController.toolbarInterpolation_ClickedCallback ( options )

Function to set the state of the interpolation button in the toolbar.

When the 'options' variable is omitted the function works as a standard callback and changes the type of interpolation: 'shape' or 'line'. However, when 'options' are specified the function sets the state of the button to the currently selected type.

| Examples: obj.toolbarInterpolation_ClickedCallback('keepcurrent'); // call from mibController; update the interpolation button icon

Parameters

options

[optional],

when 'keepcurrent' set the state of the button to the currently selected type of the interpolation.

References mibPath.

◆ toolbarRedo_ClickedCallback()

function mibController.toolbarRedo_ClickedCallback ( )

do one step forward in the undo history

◆ toolbarResizingMethod_ClickedCallback()

function mibController.toolbarResizingMethod_ClickedCallback ( options )

Function to set type of image interpolation for the visualization.

When the 'options' variable is omitted the function works as a standard callback and changes the type of image interpolation: 'bicubic' or 'nearest'. However, when 'options' are specified the function sets the state of the button to the currently selected type.

Parameters

options

[optional],

when 'keepcurrent' set the state of the button to the currently selected type of the interpolation: obj.mibModel.preferences.System.ImageResizeMethod

Examples:

obj.toolbarResizingMethod('keepcurrent'); // call from mibController; update the image interpolation button icon

◆ toolbarUndo_ClickedCallback()

function mibController.toolbarUndo_ClickedCallback ( )

do one step back in the undo history

◆ toolbarVirtualMode_ClickedCallback()

function newMode = mibController.toolbarVirtualMode_ClickedCallback ( options )

Function to switch between loading datasets to memory or reading them from HDD on demand.

When the 'options' variable is omitted the function works as a standard callback and changes the image loading mode: memory or hdd However, when 'options' are specified the function sets the state of the button to the currently selected type.

| Examples: obj.toolbarVirtualMode_ClickedCallback(); // call from mibController; switch the mode

Parameters

options

[optional],

when 'keepcurrent' set the state of the button to the currently selected in mibImage.Virtual.virtual
when 0 - uses the memory-resident mode, i.e. when the images loaded to memory
when 1 - uses the HDD-resident mode (virtual stacking), i.e. when the images kept on a hard drive

Return values

newMode

result of the function,

[] - nothing was changed
0 - switched to the memory-resident mode
1 - switched to the virtual stacking mode

References mibPath, and handle.notify.

◆ updateAxesLimits()

function mibController.updateAxesLimits	(	mode,
		index,
		newMagFactor )

Updates the obj.mibImage.axesX and obj.mibImage.axesY during fit screen, resize, or new dataset drawing.

Parameters

mode	update mode `resize` -> [default] scale to width/height `zoom` -> scale during the zoom
index	[optional] index of the mibImage to update, when [] updates the currently selected dataset
newMagFactor	a value of the new magnification factor, only for the `zoom` mode Return values:

Examples:

obj.updateAxesLimits('zoom', newMagFactor); // call from mibController; update the axes using new magnification value

obj.updateAxesLimits('resize'); // call from mibController; to fit the screen

References handle.notify.

◆ updateFilelist()

function mibController.updateFilelist ( filename )

Update list of files in the current working directory (obj.mibModel.myPath)

Parameters

filename [optional], when specified highlight filename in the list of files

◆ updateGuiWidgets()

function mibController.updateGuiWidgets ( )

Update user interface widgets in obj.mibView.gui based on the properties of the opened dataset.

References max, mibPath, min, and handle.notify.

◆ updateMyPath()

function mibController.updateMyPath ( myPath )

update mibModel.myPath, which is the current working directory

Parameters

myPath a new path to use as the working directory

Examples:

mibController.updateMyPath('c:\temp'); // set c:\temp as a new working directory

◆ updateSegmentationTable()

function mibController.updateSegmentationTable ( position )

Update obj.mibView.handles.mibSegmentationTable in the main window of mibGIU.m.

Parameters

position

[optional] a string with scroll value for the segmentation table:

current - [default] keep current position
first - scroll to the first row
end - scroll to the last row

◆ updateShownId()

function mibController.updateShownId ( Id )

update index of the displayed dataset, after, for example press of the handles.mibBufferToggle buttons in mibGUI

Parameters

Id	index of the dataset

Examples:

obj.updateShownId(str2double(Id)); // a call from obj.mibBufferToggle_Callback

References handle.notify.

◆ volren_scrollWheelFcn()

function mibController.volren_scrollWheelFcn ( eventdata )

callback for mouse wheel during the volume rendering mode

Required fields of eventdata:

◆ volren_WindowButtonDownFcn()

function mibController.volren_WindowButtonDownFcn ( )

callback for the press of a mouse button during the volume rendering mode

◆ volren_WindowButtonUpFcn()

function mibController.volren_WindowButtonUpFcn ( )

callback for mouse button up event during the volume rendering mode

◆ volren_WindowInteractMotionFcn()

function mibController.volren_WindowInteractMotionFcn ( seltype )

callback for translation/rotation of dataset during the volume rendering mode

Parameters

seltype

a string with parameter

normal - rotation mode
alt - pan/translation mode

References M.

◆ volren_winMouseMotionFcn()

function mibController.volren_winMouseMotionFcn ( )

change cursor shape when cursor is inside the axis during the volume rendering mode

◆ volrenToolbarSwitch_ClickedCallback()

function mibController.volrenToolbarSwitch_ClickedCallback ( parameter )

a callback for press of obj.mibView.volrenToolbarSwitch in the toolbar of MIB

Parameters

parameter

a string

toolbar - specify that the function was triggered by pressing a dedicated button in MIB toolbar

References makeViewMatrix(), max, and mibResize3d().

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Member Data Documentation

◆ brushSizeNumbers

mibController.brushSizeNumbers

matrix with the font for changing of brush size

◆ childControllers

mibController.childControllers

list of opened subcontrollers

◆ childControllersIds

mibController.childControllersIds

a cell array with names of initialized child controllers

◆ DragNDrop

mibController.DragNDrop

drag and drop handle for dropping the files to the file listbox

Referenced by mibDragAndDropFiles(), and mibDragAndDropModelFiles().

◆ DragNDropModel

mibController.DragNDropModel

drag and drop handle for dropping the files to the file listbox

◆ listener

mibController.listener

a cell array with handles to listeners

◆ matlabVersion

mibController.matlabVersion

version of Matlab

◆ mibModel

mibController.mibModel

handles to the model

Referenced by mibRoiRegion.addROIsToPlot(), mibMeasure.AngleFun(), mibMeasure.CaliperFun(), mibMeasure.CircleFun(), mibMeasure.DistanceFreeFun(), mibMeasure.DistanceFun(), mibMeasure.DistancePolyFun(), mibMeasure.drawROI(), mibRoiRegion.drawROI(), mibMeasure.editMeasurements(), mibRoiRegion.imellipseFun(), mibRoiRegion.impolyFun(), mibRoiRegion.imrectFun(), mibController(), and mibMeasure.PointFun().

◆ mibPath

mibController.mibPath

path to MIB installation directory

Referenced by getDefaultParameters(), menuDatasetScalebar_Callback(), menuDatasetTrasform_Callback(), menuFileImportImage_Callback(), menuFileRender_Callback(), menuImageToolsProjection_Callback(), menuMaskExport_Callback(), menuMaskImageReplace_Callback(), menuMaskImport_Callback(), menuModelAnn_Callback(), menuModelsImport_Callback(), mibAddMaterialBtn_Callback(), mibBrushPanelInterpolationSettingsBtn_Callback(), mibBufferToggleContext_Callback(), mibController(), mibFijiExport(), mibFijiImport(), mibFileFilterPopup_cm(), mibFilesListbox_Callback(), mibFilesListbox_cm_Callback(), mibGUI_WindowButtonUpFcn(), mibRemoveMaterialBtn_Callback(), mibRoiList_cm_Callback(), mibSegmentationAnnotation(), mibSegmentationTable_cm_Callback(), mibSegmSAMPanel_Callbacks(), mibShowMilestoneDialog(), toolbarCenterPointShow_ClickedCallback(), toolbarInterpolation_ClickedCallback(), toolbarVirtualMode_ClickedCallback(), and updateGuiWidgets().

◆ mibVersion

mibController.mibVersion

= ver. 2.601 / 04.11.2019; % ATTENTION! it is important to have the version number between "ver." and "/" version of MIB

Referenced by mibController().

◆ mibVersionNumeric

mibController.mibVersionNumeric

version of MIB in numerical form

◆ mibView

mibController.mibView

handle to the view

Referenced by mibRoiRegion.addROIsToPlot(), mibMeasure.AngleFun(), mibMeasure.CaliperFun(), mibMeasure.CircleFun(), mibMeasure.DistanceFun(), mibMeasure.DistancePolyFun(), mibMeasure.drawROI(), mibRoiRegion.drawROI(), mibRoiRegion.imellipseFun(), mibRoiRegion.impolyFun(), mibRoiRegion.imrectFun(), mibController(), and mibMeasure.PointFun().

The documentation for this class was generated from the following files:

Classes/@mibController/mibController.m
Classes/@mibController/devTest_ClickedCallback.m
Classes/@mibController/exitProgram.m
Classes/@mibController/findChildId.m
Classes/@mibController/getDefaultParameters.m
Classes/@mibController/getMeta.m
Classes/@mibController/imageRedraw.m
Classes/@mibController/menuDatasetParameters_Callback.m
Classes/@mibController/menuDatasetScalebar_Callback.m
Classes/@mibController/menuDatasetSlice_Callback.m
Classes/@mibController/menuDatasetTrasform_Callback.m
Classes/@mibController/menuFileChoppedImage_Callback.m
Classes/@mibController/menuFileExamples_Callback.m
Classes/@mibController/menuFileExportImage_Callback.m
Classes/@mibController/menuFileImportImage_Callback.m
Classes/@mibController/menuFilePreference_Callback.m
Classes/@mibController/menuFileRender_Callback.m
Classes/@mibController/menuFileSaveImageAs_Callback.m
Classes/@mibController/menuImageColorCh_Callback.m
Classes/@mibController/menuImageContrast_Callback.m
Classes/@mibController/menuImageIntensity_Callback.m
Classes/@mibController/menuImageInvert_Callback.m
Classes/@mibController/menuImageMode_Callback.m
Classes/@mibController/menuImageToolsContentAware_Callback.m
Classes/@mibController/menuImageToolsProjection_Callback.m
Classes/@mibController/menuMaskExport_Callback.m
Classes/@mibController/menuMaskImageReplace_Callback.m
Classes/@mibController/menuMaskImport_Callback.m
Classes/@mibController/menuMaskInvert_Callback.m
Classes/@mibController/menuMaskLoad_Callback.m
Classes/@mibController/menuMaskSaveAs_Callback.m
Classes/@mibController/menuModelAnn_Callback.m
Classes/@mibController/menuModelsExport_Callback.m
Classes/@mibController/menuModelsImport_Callback.m
Classes/@mibController/menuModelsRender_Callback.m
Classes/@mibController/menuModelsSaveAs_Callback.m
Classes/@mibController/menuSelectionBuffer_Callback.m
Classes/@mibController/menuSelectionInterpolate.m
Classes/@mibController/menuSelectionToMaskBorder_Callback.m
Classes/@mibController/menuToolsMeasure_Callback.m
Classes/@mibController/mibAddMaterialBtn_Callback.m
Classes/@mibController/mibAnisotropicDiffusion.m
Classes/@mibController/mibAnnMarkerEdit_Callback.m
Classes/@mibController/mibAutoBrightnessBtn_Callback.m
Classes/@mibController/mibBioformatsCheck_Callback.m
Classes/@mibController/mibBrushPanelInterpolationSettingsBtn_Callback.m
Classes/@mibController/mibBrushSuperpixelsEdit_Callback.m
Classes/@mibController/mibBrushSuperpixelsWatershedCheck_Callback.m
Classes/@mibController/mibBufferToggle_Callback.m
Classes/@mibController/mibBufferToggleContext_Callback.m
Classes/@mibController/mibChangeLayerEdit_Callback.m
Classes/@mibController/mibChangeLayerSlider_Callback.m
Classes/@mibController/mibChangeTimeEdit_Callback.m
Classes/@mibController/mibChangeTimeSlider_Callback.m
Classes/@mibController/mibChannelMixerTable_Callback.m
Classes/@mibController/mibChannelMixerTable_CellEditCallback.m
Classes/@mibController/mibChannelMixerTable_CellSelectionCallback.m
Classes/@mibController/mibColChannelCombo_Callback.m
Classes/@mibController/mibCreateModelBtn_Callback.m
Classes/@mibController/mibDoUndo.m
Classes/@mibController/mibDragAndDropFiles.m
Classes/@mibController/mibDragAndDropModelFiles.m
Classes/@mibController/mibEraserEdit_Callback.m
Classes/@mibController/mibFijiExport.m
Classes/@mibController/mibFijiImport.m
Classes/@mibController/mibFijiRunMacro.m
Classes/@mibController/mibFileFilterPopup_cm.m
Classes/@mibController/mibFilesListbox_Callback.m
Classes/@mibController/mibFilesListbox_cm_Callback.m
Classes/@mibController/mibFindMaterialUnderCursor.m
Classes/@mibController/mibGUI_Brush_scrollWheelFcn.m
Classes/@mibController/mibGUI_panAxesFcn.m
Classes/@mibController/mibGUI_PanelShiftBtnUpFcn.m
Classes/@mibController/mibGUI_ScrollWheelFcn.m
Classes/@mibController/mibGUI_SizeChangedFcn.m
Classes/@mibController/mibGUI_WindowBrushMotionFcn.m
Classes/@mibController/mibGUI_WindowButtonDownFcn.m
Classes/@mibController/mibGUI_WindowButtonUpDragAndDropFcn.m
Classes/@mibController/mibGUI_WindowButtonUpFcn.m
Classes/@mibController/mibGUI_WindowDragAndDropMotionFcn.m
Classes/@mibController/mibGUI_WindowKeyPressFcn.m
Classes/@mibController/mibGUI_WindowKeyPressFcn_BrushSuperpixel.m
Classes/@mibController/mibGUI_WindowKeyReleaseFcn.m
Classes/@mibController/mibGUI_WinMouseMotionFcn.m
Classes/@mibController/mibImageFilterDoitBtn_Callback.m
Classes/@mibController/mibLoadModelBtn_Callback.m
Classes/@mibController/mibLutCheckbox_Callback.m
Classes/@mibController/mibMaskedAreaCheck_Callback.m
Classes/@mibController/mibMaskGenerator.m
Classes/@mibController/mibMaskRecalcStatsBtn_Callback.m
Classes/@mibController/mibMaskShowCheck_Callback.m
Classes/@mibController/mibModelPropertyUpdate.m
Classes/@mibController/mibModelShowCheck_Callback.m
Classes/@mibController/mibPixelInfo_Callback.m
Classes/@mibController/mibRecolorLabels.m
Classes/@mibController/mibRemoveMaterialBtn_Callback.m
Classes/@mibController/mibRoiAddBtn_Callback.m
Classes/@mibController/mibRoiList_cm_Callback.m
Classes/@mibController/mibRoiLoadBtn_Callback.m
Classes/@mibController/mibRoiOptionsBtn_Callback.m
Classes/@mibController/mibRoiRemoveBtn_Callback.m
Classes/@mibController/mibRoiSaveBtn_Callback.m
Classes/@mibController/mibRoiShowCheck_Callback.m
Classes/@mibController/mibRoiToSelectionBtn_Callback.m
Classes/@mibController/mibSegmAnnDeleteAllBtn_Callback.m
Classes/@mibController/mibSegmentation3dBall.m
Classes/@mibController/mibSegmentationAnnotation.m
Classes/@mibController/mibSegmentationBlackWhiteThreshold.m
Classes/@mibController/mibSegmentationBrush.m
Classes/@mibController/mibSegmentationDragAndDrop.m
Classes/@mibController/mibSegmentationLasso.m
Classes/@mibController/mibSegmentationLassoManual.m
Classes/@mibController/mibSegmentationLines3D.m
Classes/@mibController/mibSegmentationMagicWand.m
Classes/@mibController/mibSegmentationMembraneClickTraker.m
Classes/@mibController/mibSegmentationObjectPicker.m
Classes/@mibController/mibSegmentationPanelCheckboxes.m
Classes/@mibController/mibSegmentationRegionGrowing.m
Classes/@mibController/mibSegmentationSAM.m
Classes/@mibController/mibSegmentationSAM2.m
Classes/@mibController/mibSegmentationSAM_requirements.m
Classes/@mibController/mibSegmentationSpot.m
Classes/@mibController/mibSegmentationTable_CellSelectionCallback.m
Classes/@mibController/mibSegmentationTable_cm_Callback.m
Classes/@mibController/mibSegmentationToolPopup_Callback.m
Classes/@mibController/mibSegmFavToolCheck_Callback.m
Classes/@mibController/mibSegmSAMPanel_Callbacks.m
Classes/@mibController/mibSegmSelectedOnlyCheck_Callback.m
Classes/@mibController/mibSelectionButton_Callback.m
Classes/@mibController/mibSelectionClearBtn_Callback.m
Classes/@mibController/mibSelectionDilateBtn_Callback.m
Classes/@mibController/mibSelectionErodeBtn_Callback.m
Classes/@mibController/mibSelectionFillBtn_Callback.m
Classes/@mibController/mibSelectionPanelCheckboxes.m
Classes/@mibController/mibShowMilestoneDialog.m
Classes/@mibController/mibToolbar_ZoomBtn_ClickedCallback.m
Classes/@mibController/mibToolbarPlaneToggle.m
Classes/@mibController/mibUpdatePresetFromSegmentationSettings.m
Classes/@mibController/mibUpdateSegmentationSettingsFromPreset.m
Classes/@mibController/mibViewSettingsPanelCheckboxes.m
Classes/@mibController/mibZoomEdit_Callback.m
Classes/@mibController/plotImage.m
Classes/@mibController/redrawMibChannelMixerTable.m
Classes/@mibController/setMeta.m
Classes/@mibController/startController.m
Classes/@mibController/startPlugin.m
Classes/@mibController/toolbarBlockModeSwitch_ClickedCallback.m
Classes/@mibController/toolbarCenterPointShow_ClickedCallback.m
Classes/@mibController/toolbarInterpolation_ClickedCallback.m
Classes/@mibController/toolbarRedo_ClickedCallback.m
Classes/@mibController/toolbarResizingMethod_ClickedCallback.m
Classes/@mibController/toolbarUndo_ClickedCallback.m
Classes/@mibController/toolbarVirtualMode_ClickedCallback.m
Classes/@mibController/updateAxesLimits.m
Classes/@mibController/updateFilelist.m
Classes/@mibController/updateGuiWidgets.m
Classes/@mibController/updateMyPath.m
Classes/@mibController/updateSegmentationTable.m
Classes/@mibController/updateShownId.m
Classes/@mibController/volren_scrollWheelFcn.m
Classes/@mibController/volren_WindowButtonDownFcn.m
Classes/@mibController/volren_WindowButtonUpFcn.m
Classes/@mibController/volren_WindowInteractMotionFcn.m
Classes/@mibController/volren_winMouseMotionFcn.m
Classes/@mibController/volrenToolbarSwitch_ClickedCallback.m

Public Member Functions

Static Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ mibController()

Member Function Documentation

◆ devTest_ClickedCallback()

◆ exitProgram()

◆ findChildId()

◆ getDefaultParameters()

◆ getMeta()

◆ imageRedraw()

◆ Listner2_Callback()

◆ listner_ModelEvent_Callback()

◆ menuDatasetParameters_Callback()

◆ menuDatasetScalebar_Callback()

◆ menuDatasetSlice_Callback()

◆ menuDatasetTrasform_Callback()

◆ menuFileChoppedImage_Callback()

◆ menuFileExamples_Callback()

◆ menuFileExportImage_Callback()

◆ menuFileImportImage_Callback()

◆ menuFilePreference_Callback()

◆ menuFileRender_Callback()

◆ menuFileSaveImageAs_Callback()

◆ menuImageColorCh_Callback()

◆ menuImageContrast_Callback()

◆ menuImageIntensity_Callback()

◆ menuImageInvert_Callback()

◆ menuImageMode_Callback()

◆ menuImageToolsContentAware_Callback()

◆ menuImageToolsProjection_Callback()

◆ menuMaskExport_Callback()

◆ menuMaskImageReplace_Callback()

◆ menuMaskImport_Callback()

◆ menuMaskInvert_Callback()

◆ menuMaskLoad_Callback()

◆ menuMaskSaveAs_Callback()

◆ menuModelAnn_Callback()

◆ menuModelsExport_Callback()

◆ menuModelsImport_Callback()

◆ menuModelsRender_Callback()

◆ menuModelsSaveAs_Callback()

◆ menuSelectionBuffer_Callback()

◆ menuSelectionInterpolate()

◆ menuSelectionToMaskBorder_Callback()

◆ menuToolsMeasure_Callback()

◆ mibAddMaterialBtn_Callback()

◆ mibAnisotropicDiffusion()

◆ mibAnnMarkerEdit_Callback()

◆ mibAutoBrightnessBtn_Callback()

◆ mibBioformatsCheck_Callback()

◆ mibBrushPanelInterpolationSettingsBtn_Callback()

◆ mibBrushSuperpixelsEdit_Callback()

◆ mibBrushSuperpixelsWatershedCheck_Callback()

◆ mibBufferToggle_Callback()

◆ mibBufferToggleContext_Callback()

◆ mibChangeLayerEdit_Callback()

◆ mibChangeLayerSlider_Callback()

◆ mibChangeTimeEdit_Callback()

◆ mibChangeTimeSlider_Callback()

◆ mibChannelMixerTable_Callback()

◆ mibChannelMixerTable_CellEditCallback()

◆ mibChannelMixerTable_CellSelectionCallback()

◆ mibColChannelCombo_Callback()

◆ mibCreateModelBtn_Callback()

◆ mibDoUndo()

◆ mibDragAndDropFiles()

◆ mibDragAndDropModelFiles()

◆ mibEraserEdit_Callback()

◆ mibFijiExport()

◆ mibFijiImport()

◆ mibFijiRunMacro()

◆ mibFileFilterPopup_cm()

◆ mibFilesListbox_Callback()

◆ mibFilesListbox_cm_Callback()

◆ mibFindMaterialUnderCursor()

◆ mibGUI_Brush_scrollWheelFcn()

◆ mibGUI_panAxesFcn()