< Master index Index for ./cellorganizer/utilities >

Index for ./cellorganizer/utilities

Matlab files in this directory:

 AdjustResolutionsADJUSTRESOLUTIONS resized a 3D image according to the input and output resolutions given
 create_sphereMYSPHERE Helper method that creates a 3d sphere image
 demo2htmlDEMO2HTML Returns projection images and html file
 findObjFitRegion - binary mask of area to place objects, to be eroded by objWeight
 findTagFINDTAG Returns the starting indexes of all the occurrences of tag within
 fixadherentFIXADHERENT forces an adherent cell to have its largest slice on the bottom of the segmented cell
 getMeanModelCompute (weighted) average model
 getMeshPointsGETMESHPOINTS This function gets mesh points given an image
 hasToolboxHASTOOLBOX True iff the current system has the Matlab toolbox available,
 img2modelIMG2MODEL Trains a generative model of protein subcellular location from a
 img2tifIMG2TIF Saves an image to a multichannel tiff. Input argument
 img2xmlINDEX2XML Converts an indexed image to a sparse matrix, and saves as an xml
 improjIMGPROJ Wrapper method for img2projection. Input argument img can
 ims2indexIMG2INDEX Converts an intensity image into an indexed image.
 instance2SBMLINSTANCE2SBML Writes data struct to a SBML-Spatial file. If an existing file is provided
 make_intermediate_results_from_temp_folderMAKE_INTERMEDIATE_RESULTS_FROM_TEMP_FOLDER Helper method that takes files
 mathml2arrayMATHML2ARRAY Parses a MathML vector or array into a Matlab array.
 matrixMATRIX Helper function that handles the reading of MathML matrices in
 ml_findmainobjfinds the largest non-zero pixel region in an image
 ml_initparamTZ_INITPARAM Initialize parameters.
 ml_loadimageML_LOADIMAGE Read images under one directory into a 3D matrix.
 ml_lsFILELISTING = ML_LS( PATTERN ) Returns file listing of wildcard PATTERN (e.g. '*.jpg').
 ml_saveimageML_SAVEIMAGE Saves images according to the Murphylab title format for easy reading by
 model2diffeomorphicInstanceMODEL2DIFFEORMORPHICINSTANCE Helper method that synthesizes a framework
 model2frameworkMODEL2FRAMEWORK Helper method that generates a 2D/3D framework from a
 model2imgMODEL2IMG Synthesizes a multicolor image from a set of SLML Level 1.0
 model2instanceMODEL2INSTANCE Generate a single instance from a valid SLML model.
 model2report_percellFunction that creates useful reports on percell statistics
 models2reportMODELS2REPORT Generate a report comparing various SLML models.
 moveObjectsMOVEOBJECTS This function moves object positions according to the specified parameters
 niceplotNICEPLOT Helper function to plot something that is readable and savable in a new figure window.
 objectMovementModelOBJECTMOVEMENTMODEL creates random walks for each object within a cell ignoring conflicts with other objects and cell/nuclear boundaries.
 pc12_cropImgPC12_CROPIMG Automatically crops images
 plotcylsurfCopyright (C) 2007-2013 Murphy Lab
 plotmodelsgrj 16/5/2013
 plotmodelsparamPLOTMODELSPARAM plots the independent variable, x, against the models struct component, modelVar.
 preprocessPREPROCESS segments and preprocesses a given image.
 print2filePRINT2FILE Helper function that prints the contents of an array on a
 print2screenPRINT2SCREEN Helper function that prints the contents of an array on the
 set_temp_result_foldersSET_TEMP_RESULT_FOLDERS checks the param struct for user defined temp directories, if not
 slml2reportSLML2REPORT Generate a report comparing various SLML models.
 splashSPLASH MATLAB code for splash.fig
 tif2imgTIF2IMG Reads a multichannel tif and loads the image to workspace.

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