Main Functions

Note

This section only includes the headers of the most important functions in CellOrganizer.

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.<name>      Holds the value of variable <name>. 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.

slml2info

Method header:

% SLML2INFO Generate a report from information extracted from a genearative model file
%
% List Of Input Arguments  Descriptions
% -----------------------  ------------
% filename                 Model filename
% options                  Options structure
%
% Example
% > filename = '/path/to/model/file/model.mat';
% > answer = slml2info( filename );

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;

slml2report

Method header:

% SLML2REPORT Generate a report comparing two SLML generative models
%
% List Of Input Arguments  Descriptions
% -----------------------  ------------
% model1                   A generative model filename
% model2                   A generative model filename
%
% Example
% > filename1 = '/path/to/model/model1.mat';
% > filename2 = '/path/to/model/model2.mat';
% answer = slml2report( filename1, filename2 );

slml2slml

Method header:

function model = slml2slml( varargin )
% SLML2SLML Combines multiple SLML files into a single model file.
%
% List Of Input Arguments     Descriptions
% -----------------------     ------------
% files                       list of paths of models need be combined
% options                     Options structure
%
% The input argument options holds the valid parameters for these components.
% The shape of options is described below
%
% List Of Parameters        Descriptions
% ------------------        ------------
% output_filename           (optional)the file name of output model,
%                           default is "model.mat"
% seletion
% name
%
% Documentation (optional)
% ------------------------
% This is an optional structure with multiple elements that holds documentation about this model.
% If the decumentation isn't input, function will inherit documentation from first
% model in list if model is present.