.. api: API === .. note:: This section only includes the headers of the most important functions in CellOrganizer. This is the documentation included with the main methods im2blender ********** Method header:: function [shiftvector, answer] = im2blender( img, savefile, downsample, patchsample, shiftvector_flag) % IMG2BLENDER Exports a generated instance from CellOrganizer to a .obj mesh format % that can be read by Blender. % % % List Of Input Arguments Descriptions % ----------------------- ------------ % img a 3D image you wish to obtain the mesh for % downsample factor by which you wish to downsample % savefile the path and file name you wish to save the generated file as % patchsample the percentage of the verticies calculated that the user % wants kept. Keeping more will result in a larger .obj file but have % better resolution. Default value is 0.05 % shiftvector a 1x3 vector of the amount to shift the resulting mesh. % % This is used to place the mesh at the origin when called with syn2blender. % % List Of Outputs Descriptions % --------------- ------------ % shiftvector a 1x3 vector of the amount to shift the resulting mesh. % answer boolean flag that indicates if the test was successful im2projection ************* Method header:: function out_img = im2projection( img, options ) % IM2GPROJECTION creates a sum or mean projection of the input image % % List Of Input Arguments Descriptions % ----------------------- ------------ % img 3D binary or realvalued image. % options struct with a 'method' field that can be set % to 'mean' if a mean value projection is desired % % List Of Outputs Descriptions % --------------- ------------ % out_img a 2D image that contains a projection % in each dimension of the original image im2reshape ********** Method header:: function img = im2reshape( img ) % IM2RESHAPE Reshapes a 3D images into a 2D representation % % List Of Input Arguments Descriptions % ----------------------- ------------ % img a 3D binary or realvalued image % % List Of Outputs Descriptions % --------------- ------------ % img a 2D representation of the image img2slml ******** Method header:: % IMG2SLML Trains a generative model of protein subcellular location from a % collection of microscope images and saves the model as an SLML instance. % % An SLML model consists of four components, % 1) a (optional) documentation component % 2) a nuclear pattern model, % 3) a cell pattern model and, % 4) a protein pattern model. % % List Of Input Arguments Descriptions % ----------------------- ------------ % dimensionality 2D/3D % dnaImagesDirectoryPath DNA images collection directory % cellImagesDirectoryPath Cell images collection directory % proteinImagesDirectoryPath Protein images collection directory % options Options structure % % The input argument options holds the valid parameters for these components. % The shape of options is described below % % List Of Options Descriptions % --------------- ------------ % % Mandatory options % ----------------- % model.resolutions Any double 1x2/1x3 double vector. % (microns/voxel). % % generic model options % --------------------- % masks (optional) Masks collection directory. % % train.flag (optional) Selects what model is going to be trained ('nuclear', % 'framework', or 'all'). Default is 'all'. % % model.name (optional) Holds the name of the model. Default is empty. % model.id (optional) Holds the id of the model. Default is empty. % model.filename Holds the output filename. % model.resolution Model resolution (in microns per pixel). This % the resolution of the dataset used to train the model % downsampling Downsampling vector used during preprocessing. Default value is % [5 5 1]. Final model resolution will be resolution * downsampling % vector and will be saved in the model as well % % Nuclear shape model options % --------------------------- % nucleus.type Holds the nuclear model type. Default is % "medial axis" for 2D and "cylindrical_surface" for 3D % nucleus.name (optional) Holds the name of the nuclear model. Default is empty. % nucleus.id (optional) Holds the id of the nuclear model. Default is empty. % % Cell shape model options % ------------------------ % cell.type Holds the cell model type. Default is "ratio". % cell.name (optional) Holds the name of the cell model. Default is empty. % cell.id (optional) Holds the id the cell model. Default is empty. % % Protein shape model options % --------------------------- % protein.type (optional) Holds the protein model type. The default is "vesicle". % protein.name (optional) Holds the name of the protein model. The default is empty. % protein.id (optional) Holds the id of the protein model. The default is empty. % protein.class Holds the protein class, e.g. lysosome, endosome. % protein.cytonuclearflag (optional) Determines whether the protein pattern will be generated in % the cytosolic space ('cyto'), nuclear space ('nuc') or everywhere ('all'). % Default is cyto. % % Documentation (optional) % ------------------------ % This is an optional structure with multiple elements that holds documentation about this model. % % documentation. Holds the value of variable . This is meant to be meta information. Default is empty. % % Helper Options % ------------- % verbose (optional) Displays messages to screen. Default is true. % debug (optional) Reports errors and warnings. Default is false. slml2img ******** Method header:: % SLML2IMG Synthesizes an image from a list of SLML models. % % Instances may be saved in the following forms: % a) tiff stacks: a 3D tiff image stack for each pattern generated using the input models % b) indexed images: a single 3D tiff image stack where each pattern is represented by a number 1-n % c) object mesh: a .obj mesh file for each pattern generated using the input models (blenderfile option) % d) SBML-Spatial file: a Systems Biology Markup Language (SBML) instance XML file utilizing the Spatial extension in level 3 version 1 % % % List Of Input Arguments Descriptions % ----------------------- ------------ % models A cell array of filenames % options A structure holding the function options % % The shape of options is described % % List Of Options Descriptions % --------------- ------------ % targetDirectory (optional) Directory where the images are going to be saved. Default is current directory. % prefix (optional) Filename prefix for the synthesized images. Default is 'demo' % numberOfSynthesizedImages (optional) Number of synthesized images. Default is 1. % compression (optional) Compression of tiff, i.e. 'none', 'lzw' and 'packbits' % microscope (optional) Microscope model from which we select a point spread function. Default is 'none' % synthesis (optional) Synthesis parameter that allows to % synthesize 'nucleus', 'framework' or 'all'. Default is 'all' % protein.cytonuclearflag (optional) Defines the allowable region for protein placement. % The default is the cytonuclearflag included in the model. % sampling.method (optional) Can be 'disc', 'sampled' or 'trimmed'. Default is trimmed % savePDF (optional) Saves the probability density function for a given pattern during 2D synthesis. Default is false. % spherical_cell (optional) Boolean flag that indicates whether a cell is spherical. Default is false. % overlapsubsize (optional) Defines the downsampling fraction to perform during object overlap avoidance. Default is 0.3. % overlapthresh (optional) Defines the amount of overlap that is allowed between objects. Default is 1. % rendAtStd (optional) Defines the number of standard deviations to render Gaussian objects at. Default is 2. % sampling.method.density (optional) An integer. Default is empty. % protein.cytonuclearflag (optional) Can 'cyto', 'nucleus' or 'all'. Default is all. % resolution.cell (optional) The resolution of the cell and nucleus that are being passed in % resolution.objects (optional) The resolution of the object model being synthesized % instance.cell (optional) A binary cell image to be filled with objects. Default is empty. % instance.nucleus (optional) A binary nuclear image to be filled with objects. Default is empty. % image_size (optional) The image size. Default is [1024 1024] for both 2D and 3D in x and y % synthesis.diffeomorphic.maximum_iterations (optional) Integer defining the maximum number of iterations during diffeo inference. Default is 100. % % Random walk options % ------------------- % randomwalk (optional) Boolean flag of whether to perform a shape space walk. Default is False. % framefolder (optional) The folder in which to look for completed frames and save finished frames from the diffeomorphic synthesis. % The default is './frames/'. % walksteps (optional) The integer number of steps to walk during a shape space walk. Default is 1. % walk_type (optional) Type of random walk to perform. Default is 'willmore'. % % Helper options % -------------- % % debug (optional) Keeps temporary results and catches % errors with full reports. Default is false; % display (optional) Will make pretty plots. Turning this % flag on will slow down synthesis. Default is % false. % verbose (optional) Print the intermediate steps to screen. Default is false. % % Outputs % ------- % output.tifimages (optional) Boolean flag specifying whether to write out tif images. Default is true. % output.indexedimage (optional) Boolean flag specifying whether to write out indexed image. Default is false. % output.blenderfile (optional) Boolean flag specifying whether to write out (.obj) files for use in blender. Default is false; % output.blender.downsample (optional) ownsampling fraction for the creation of object files (1 means no downsampling, 1/5 means 1/5 the size). % output.SBML (optional) boolean flag specifying whether to write out (.xml) files with SBML-Spatial representations of geometries. Default is false; syn2projection ************** Method header:: % SYN2PROJECTION Makes projections from a set of images synthesized by % CellOrganizer % % % List Of Input Arguments Descriptions % ----------------------- ------------ % imgfolder a folder of synthesized images by CellOrganizer % outputfolder the path where you wish to save the generated files % % Options structure description % % List Of Options Descriptions % --------------- ------------ % method (optional) either a sum or mean. default is sum % verbose (optional) verbose flag that displays progress % debug (optional) flag that displays debugging messages. default is false % % List Of Outputs Descriptions % --------------- ------------ % answer true if it saves all projections to disk syn2surfaceplot *************** Method header:: function syn2surfaceplot( directory, colors, viewangles, alphaval) % SYN2SURFACEPLOT Helper method that displays images generated by CellOrganizer % % List Of Input Arguments Descriptions % ----------------------- ------------ % directory a directory containing images from CellOrganizer % colors a cell array containing a list of valid colors as defined by Matlab % http://www.mathworks.com/help/techdoc/ref/colorspec.html % viewangles a vector defining the viewing angle as defined by Matlab % http://www.mathworks.com/help/techdoc/ref/view.html % alphaval a value that determines the transparency of an object % http://www.mathworks.com/help/techdoc/ref/alpha.html