Main Functions¶
Note
This section only includes the headers of the most important functions in CellOrganizer.
img2slml¶
Method header:
function answer = img2slml( varargin )
% IMG2SLML Trains a generative model of subcellular location from a
% collection of images and saves the model to disk.
%
% A CellOrganizer model consists of four components,
%
% 1) a (optional) documentation component
% 2) a nuclear membrane model,
% 3) a cell membrane model and,
% 4) a protein pattern model.
%
% ┌────────────────────────┐
% │List Of Input Parameters│
% └────────────────────────┘
% Inputs Descriptions
% ------ ------------
% dimensionality 2D/3D
% dnaImagesDirectoryPath DNA images collection directory, list of files or pattern
% cellImagesDirectoryPath Cell images collection directory, list of files or pattern
% proteinImagesDirectoryPath Protein images collection directory, list of files or pattern
% options List of options
%
% The input argument options holds the valid parameters for all of these components.
%
% ┌───────────────┐
% │List Of Options│
% └───────────────┘
% Mandatory options Descriptions
% ----------------- ------------
% model.resolutions Any double 1x2/1x3 double vector.
% (microns/voxel).
%
% Generic model options Descriptions
% --------------------- ------------
% 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 a randomly generated string.
% model.filename Holds the output filename.
% downsampling Downsampling vector to be used during preprocessing.
%
% Debugging options
% -----------------
% debug If set to true, then the function will (1) keep temporary results folder, (2) will
% print information useful for debugging. Default is false.
% display If set to true, then plots useful for debugging with be open. This functionality is
% meant for debugging only, setting this to true will considerably slow down
% computation. Default is false;
% save_segmentations Will save the segmentations to the model file. Setting this option to true will create
% a considerably large file.
%
% Nuclear shape model options Descriptions
% --------------------------- ------------
% nucleus.class (mandatory) Holds the nuclear membrane model class.
% nucleus.type (mandatory) Holds the nuclear membrane model type.
% 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 a randomly generated string.
%
% Cell shape model options Descriptions
% ------------------------ ------------
% cell.class (mandatory) Holds the cell membrane model class.
% cell.type (mandatory) Holds the cell membrane model type.
% 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 Descriptions
% --------------------------- ------------
% protein.class (mandatory) Holds the protein model class.
% protein.type (mandatory) Holds the protein model type.
% protein.name (optional) Holds the name of the protein model. The default is empty.
% protein.id (optional) Holds the id of the protein model. Default is a randomly generated string.
% 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.
%
% ┌────────────────────────────────────┐
% │List Of Options per Model class/type│
% └────────────────────────────────────┘
% 2D PCA model options
% --------------------
% model.pca.latent_dim (optional) This specifies how many latent dimensions should be used for modeling
% the shape space. Valid values arepositive integers. The default is 15.
%
% 2D diffeomorphic model options
% ------------------------------
% model.diffeomorphic.distance_computing_method (optional) ‘faster'
% model.diffeomorphic.com_align (optional) 'nuc'
%
% T cell distribution model options
% ---------------------------------
% model.tcell.synapse_location (mandatory) File path to annotation of the synapse positions of the T cells as input.
% model.tcell.results_location (mandatory) File path for where the results should be saved.
% model.tcell.named_option_set (mandatory) The running choice for CellOrganizer and one sensor of two-point annotation.
% model.tcell.use_two_point_synapses (optional) Set up the mode of synapse to use, as a default, we use one-point,
% if needed you can use two-point by set up the option as true.
% model.tcell.sensor Set up protein name.
% model.tcell.timepoints_to_include (optional) If creation of models for only a subset of the time points is desired,
% edit to specify which time points to include.
% model.tcell.model_type_to_include (mandatory) Set up for model to include.
% model.tcell.infer_synapses (mandatory) true or false.
% model.tcell.adjust_one_point_alignment (optional) Set up alignment adjustment true or false.
% model.tcell.ometiff (optional) If true, then it assumes images are OME.TIFFs with annotations. Default is false.
%
% 3D SPHARM-RPDM model options
% ----------------------------
% model.spharm_rpdm.alignment_method (optional) method by which cells willbe aligned when producing shape descriptors
% The possible values are 'major_axis' (defaut) or 'foe'.
% model.spharm_rpdm.rotation_plane (optional) Dimensions of image that will used for alignment.
% The possible values are 'xy' (defaut), 'xz', 'yz' or ‘xyz'. For example,
% if ‘xy‘ is specified, each cellwill be rotated in the xy plane (around the z axis).
% model.spharm_rpdm.postprocess (optional) This specifies whether alignment and size normalization
% should be done after parameterization. The values are ‘true’ (default) and ‘false’.
% model.spharm_rpdm.maxDeg (optional) This specifies the degree up to which spherical harmonics
% should be calculated. Valid values are positive integers. The default is 31.
% model.spharm_rpdm.components (mandatory) This specifies which components should be included in the
% shape model. The valid values are {'cell'}, {'nuc'}, or {'cell', 'nuc'}.
% model.spharm_rpdm.latent_dim (optional) This specifies how many latent dimensions should be used for
% modeling the shape space. Valid values are positive integers. The default is 15.
%
% ┌─────────────┐
% │Documentation│
% └─────────────┘
% 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:
function answer = slml2info( varargin )
% SLML2INFO Generate a report from information extracted from a genearative model file
%
% List Of Input Arguments Descriptions
% ----------------------- ------------
% filenames List of files
% options Options structure
%
% Example
% > filenames = {'/path/to/model/file/model.mat'};
% > answer = slml2info( filenames );
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.