Tools Directory Reference

Directory dependency graph for Tools:

Directories
	CellMigration
	Frangi
	HistThresh
	matGeom
	mibDeepSupport
	prettify_MATLAB_html
	RandomForest
	RegionGrowing
	Supervoxels

Files
	anisodiff.m
	ANISODIFF - Anisotropic diffusion.
	bwdistsc.m
	D=BWDISTSC(BW,ASPECT) BWDISTSC computes Euclidean distance transform of a binary 3D image BW. Distance transform assigns to each pixel in BW a number that is the distance from that pixel to the nearest nonzero pixel in BW. BWDISTSC can accept a regular 2D image, a 3D array, and a cell array of 2D slices. ASPECT is a 3-component vector defining the voxel-aspect-ratio for BW. If ASPECT is not given, [1 1 1] isotropic aspect ratio is assumed.
	bwdistsc1.m
	D=BWDISTSC1(BW,ASPECT,MAXVAL) BWDISTSC1 computes Euclidean distance transform of a binary 3D image BW out to a specified value MAXVAL. This allows accelerating the calculations in some cases with strongly nonconvex geometries, if the distance transform only needs to be calculated out to a specific value. The distance transform assigns to each pixel in BW a number that is the distance from that pixel to the nearest nonzero pixel in BW. BW may be a 3D array or a cell array of 2D slices. BWDISTSC1 can also accept regular 2D images. ASPECT is a 3-component vector defining the aspect ratios to use when calculating the distances in BW. If ASPECT is not set, isotropic aspect ratio [1 1 1] is used. If MAXVAL is specified, the distance transform will be only calculated out to the value MAXVAL.
	cell2clip.m
	cell2clip copies contents of cell-array to the clipboard
	convertAbsoluteToRelativePath.m
	convert absolute path into relative path, where the part of the absolute path that is matching the relative path is replaced with the templateText.
	convertPixelsToUnits.m
	convert pixel with x, y, z coordinate to the physical imaging units
	convertRelativeToAbsolutePath.m
	convert relative path into absolute path, where the part of the relative path containing text template (templateText) will be replaced with the abosolute path
	DnD_uifigure.m
	Set up a callback when file/folder is dropped onto a uifigure component.
	editbox_Callback.m
	Check for entered values in an edit box.
	findjobj.m
	findjobj Find java objects contained within a specified java container or Matlab GUI handle
	findNode.m
	find a node in the uitree which has nodeName text in it, used by mibDatasetInfoController
	fstack.m
	Focus stacking.
	fstack_mib.m
	Extended depth-of-field focus stacking based on fstack function by Said Pertuz https://se.mathworks.com/matlabcentral/fileexchange/55115-extended-depth-of-field Generate extended depth-of-field image from focus sequence using noise-robust selective all-in-focus algorithm [1].
	generateBoxPlot.m
	generate a box plot with points
	generateDefaultKeyShortcuts.m
	generate KeyShortcuts structure with defauld key shortcuts
	GetExeLocation.c
	getPrefDir.m
	get directory where MIB preferences are stored on Windows it is C:\Users\Username\Matlab on Mac it is /Users/username/Matlab on Linux it is /home/username/Matlab
	ginputc.m
	GINPUTC Graphical input from mouse. GINPUTC behaves similarly to GINPUT, except you can customize the cursor color, line width, and line style.
	imclipboard.m
	IMCLIPBOARD Copy and paste images to and from system clipboard.
	imRAG.m
	IMRAG Region adjacency graph of a labeled image.
	imRichRAG.m
	IMRICHRAG Region adjacency graph of a labeled image with edge infos, originating from the imRAG function.
	mib_compile_c_files.m
	This script will compile all the C files get MIB directory.
	mibAddScaleBar.m
	I = mibAddScaleBar(I, pixSize, scale, orientation, scaleBarHeight) add a scale bar to the image. Requires insertText and insertMarker functions from the Computer Vision System Toolbox. When these functions are not available is using an old function.
	mibAddText2Img.m
	Add text label to the image, a new function introduced in MIB 2.22. Requires insertText and insertMarker functions from the Computer Vision System Toolbox. When these functions are not available mibAddText2Img is using an old function.
	mibAddText2Img_Legacy.m
	Add text label to the image, an older function that does not use insertText and insertMarker functions from the Computer Vision System Toolbox.
	mibAlignmentDetectFeatures.m
	detect feature points for image, this function is used in AutomaticFeatureBasedAlignment function in mibAlignmentController
	mibCalcCurveLength.m
	Calculate length of the curve objects in the slice.
	mibCalcShifts.m
	Calculate alignment shifts between slices in I.
	mibConcatenateStructures.m
	update fields of primaryStruct using the fields of secondaryStruct
	mibConnectPoints.m
	Generate a bitmap image with lines that connect points (pnts)
	mibCrossShiftStack.m
	imgOut = mibCrossShiftStack(imgIn, shiftsX, shiftsY, options) Shift stack provided in imgIn using translation numbers in shiftX and shiftY
	mibCrossShiftStacks.m
	[imgOut, bbShiftXY] = mibCrossShiftStacks(I1, I2, shiftX, shiftY) Shift I2 vs I1 using translation numbers in shiftX and shiftY
	mibDoAndiffFiltering.m
	Filter dataset with anisotropic diffusion.
	mibDoImageFiltering.m
	Filter image with basic Matlab filters.
	mibDoImageFiltering2.m
	Filter the image, alternative version of mibDoImageFiltering with more filters and BatchOpt compatible structure.
	mibElasticDistortionFilter.m
	apply elastic deformations to img, the code is based on Best Practices for Convolutional Neural Networks Applied to Visual Document Analysis by Patrice Y. Simard, Dave Steinkraus, John C. Platt http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.160.8494&rep=rep1&type=pdf https://cognitivemedium.com/assets/rmnist/Simard.pdf and codes available at
	mibGenerateDefaultSegmentationPalette.m
	generate color palette depending on the provided paletteName and required noColors
	mibGetFrangiMask.m
	Return Frangi mask generated from img.
	mibGetMorphMask.m
	Return result of BW Morphological filters generated from img.
	mibGetStrelMask.m
	Return Strel mask (imtophat/imbothat) generated from the img.
	mibGetVersionNumberic.m
	get MIB version in numeric format from the string
	mibImageProfileIntegrate.m
	calculate image intensity profile for line ROI based on code by Damien in comments of http://se.mathworks.com/matlabcentral/fileexchange/11568-extract-integrated-intensity-profiles-from-image
	mibInterpolateLines.m
	Interpolate lines between the slices.
	mibInterpolateShapes.m
	Interpolate the shapes between the slices.
	mibOscResampling.m
	resample image usng OSC method
	mibRemoveBranches.m
	remove branches from thinned bitmap image img the line can be thinned using _img = bwmorph(img, thin, Inf)_ command somewhat based on "Exploring shortest paths – part 5" by Steve Eddins (https://blogs.mathworks.com/steve/2011/12/13/exploring-shortest-paths-part-5/)
	mibRemoveSaltAndPepperNoise.m
	mibRenderModel.m
	Render a model using isosurfaces.
	mibResize3d.m
	Resize 3D dataset.
	mibRunningAverageSmoothPoints.m
	mibRunningAverageSmoothPoints - Smooth points for running average correction
	mibSaveTableToHeaderCSV.m
	Save MATLAB Table (T) to CSV file (fn) with a header standard MATLAB writetable function does not support generation of headers, this function allows to produce CSV file with header generated from table Properties.
	mibShowErrorDialog.m
	show error that is generated in try/catch blocks
	mibSubtractRunningAverage.m
	smooth drift correction using the running average correction
	mibTraceCurve.m
	Connect points with search for a minimum gradients.
	num2clip.m
	parseStructToTree.m
	function to parse structure (XML) to uitree object based on struct2xml.m file by W. Falkena, ASTI, TUDelft, 27-08-2010
	patchnormals.m
	This function PATCHNORMALS calculates the normals of a triangulated mesh. PATCHNORMALS calls the patchnormal_double.c mex function which first calculates the normals of all faces, and after that calculates the vertice normals from the face normals weighted by the angles of the faces.
	patchnormals_double.c
	patchnormals_double.m
	regionprops3mib.m
	regionprops3mib measures the geometric properties of image objects in 3D space. Objects are defined as connected pixels in 3D. This function uses regionprops to get pixellist from the binary image. If you'd like to define objects connectivity on our own, use bwlabeln first.
	saveImageParFor.m
	saveImageParFor(fn, imgOut, compressImage) saving image from parfor loop as it is not possible to use save directly inside parfor this function is used in mibDeepController to preprocess images
	showErrorDialog.m
	show error that is generated in try/catch blocks
	struct2array.m
	replacement for struct2array function that was present is Matlab before R2021b (at least)
	uigetfile_n_dir.m
	Pick multiple directories and/or files.
	updateBatchOptCombineFields_Shared.m
	a common function used by all tools compatible with the Batch mode to combine fields of the input structure BatchOptIn with fields of the default structure BatchOpt
	updateBatchOptFromGUI_Shared.m
	a common function used by all tools compatible with the Batch mode to update BatchOpt structure fields from GUI widgets
	updateGUIFromBatchOpt_Shared.m
	a common function used by all tools compatible with the Batch mode to setup widgets of GUI from the BatchOpt structure
	view3d.m
	view3d Interactively rotate, zoom and pan the view of a 3-D plot
	violin.m
	windv.m
	windv(vector, window size, asInSmooth) vectorized version of windv() smooths a vector using a window of +/- window size window size is reduced at the edges
	xlswrite2.m
	XLSWRITE Stores numeric array or cell array in Excel workbook.
	xlswrite3.m
	XLSWRITE Stores numeric array or cell array in Excel workbook.