.. demos_information: Demos ===== 2D/3D Demos *********** For convenience, a series of demos are included with each distribution of CellOrganizer. These demos show * how to synthesize images from existing models, * how to train new models from raw data, as well as * other functionality, e.g. exporting examples in multiple formats. To display information about the available demos contained in the distribution, type in Matlab terminal:: >> demoinfo For example, in Ubuntu .. raw:: html Demos Summary Table ******************* This table will let you know if the demo is meant to train a model or synthesize an image. +------------------------+---------+------------+-------------+ | Name | 2D/3D | Training | Synthesis | +========================+=========+============+=============+ | demo2D00_ | 2D | | True | +------------------------+---------+------------+-------------+ | demo2D01_ | 2D | True | | +------------------------+---------+------------+-------------+ | demo2D02_ | 2D | | True | +------------------------+---------+------------+-------------+ | demo2D03_ | 2D | True | | +------------------------+---------+------------+-------------+ | demo2D04_ | 2D | True | | +------------------------+---------+------------+-------------+ | demo2D05_ | 2D | True | | +------------------------+---------+------------+-------------+ | demo2D06_ | 2D | | True | +------------------------+---------+------------+-------------+ | demo2D07_ | 2D | | True | +------------------------+---------+------------+-------------+ | demo2D08_ | 2D | True | | +------------------------+---------+------------+-------------+ | demo2D09_ | 2D | True | | +------------------------+---------+------------+-------------+ | demo3D00_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D01_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D02_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D03_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D04_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D05_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D06_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D07_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D08_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D09_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D10_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D11_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D12_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D13_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D14_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D15_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D16_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D17_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D18_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D19_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D20_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D21_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D22_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D23_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D24_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D25_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D26_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D27_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D28_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D29_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D30_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D31_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D32_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D33_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D34_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D35_ | 3D | | | +------------------------+---------+------------+-------------+ | demo3D36_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D37_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D38_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D39_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D40_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D41_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D42_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D43_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D44_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D45_ | 3D | True | | +------------------------+---------+------------+-------------+ | demo3D46_ | 3D | | True | +------------------------+---------+------------+-------------+ | demo3D47_ | 3D | | | +------------------------+---------+------------+-------------+ Brief Descriptions ****************** .. _demo2D00: demo2D00 -------------------------------- Demo header:: % Synthesize one 2D image with nuclear, cell shape, and vesicular channels % from all vesicular object models (nucleoli, lysosomes, endosomes, and % mitochondria) without convolution. The model was trained from the Murphy % Lab 2D HeLa dataset. % % What you need % ------------- % * a list of valid CellOrganizer model files % % Output % ------ % * one TIFF file with six slices (nuclear, cell shape, nucleolar, % lysosomal, endosomal, and mitochondrial channels) Demo output: .. figure:: ../images/demo2D00/image.png :target: ../_images/demo2D00/image.png :align: center .. _demo2D01: demo2D01 -------- Demo header:: % Train 2D generative model of the nucleus, cell shape, and lysosome using % all LAMP2 images in the Murphy Lab 2D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo2D02: demo2D02 -------- Demo header:: % Synthesize one 2D image with nuclear, cell shape, and lysosomal channels % from LAMP2 model trained in demo2D01 without convolution. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * one TIFF file with three slices (nuclear, cell shape, and lysosomal % channels) Demo output: .. figure:: ../images/demo2D02/image.png :target: ../_images/demo2D02/image.png :align: center .. _demo2D03: demo2D03 -------- Demo header:: % Train 2D generative model of the nucleus, cell shape, and lysosome using % all LAMP2 images in the Murphy Lab 2D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo2D04: demo2D04 -------- Demo header:: % Train 2D generative diffeomorphic nuclear and cell shape model and a % lysosomal model using 10 LAMP2 images in the Murphy Lab 2D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo2D05: demo2D05 -------- Demo header:: % Train 2D generative pca nuclear and cell shape model using the Murphy Lab 2D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo2D06: demo2D06 -------- Demo header:: % Reconstruct one 2D image with nuclear, cell shape for PCA model % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * one TIFF file with three slices (nuclear, cell shape, and lysosomal % channels) Demo output: .. figure:: ../images/demo2D06/image.png :target: ../_images/demo2D06/image.png :align: center .. _demo2D07: demo2D07 -------- Demo header:: % Synthesize one 2D image with nuclear, cell shape with PCA model % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * one TIFF file with three slices (nuclear, cell shape, and lysosomal % channels) Demo output: .. figure:: ../images/demo2D07/image.png :target: ../_images/demo2D07/image.png :align: center .. _demo2D08: demo2D08 -------- Demo header:: % Train 2D generative pca nuclear and cell shape model using the Murphy Lab % 2D HeLa dataset and makes a shape space plot % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file % * a shape space plot .. _demo2D09: demo2D09 -------- Demo header:: % Train 2D generative pca nuclear and cell shape model using the Murphy Lab % 2D HeLa dataset and makes a shape space plot % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file % * a report .. _demo3D00: demo3D00 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and nucleolar channels % from nucleolar model with sampling method set to render nucleoli as % ellipsoids without convolution. The model was trained from the Murphy Lab % 3D HeLa dataset. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * three TIFF files (nuclear, cell shape, and nucleolar channels) .. _demo3D01: demo3D01 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and vesicular channels % from all vesicular object models (lysosomes, mitochondria, nucleoli, and % endosomes) with sampling method set to render vesicular objects as % ellipsoids without convolution. The model was trained from the Murphy Lab % 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * six TIFF files (nuclear, cell shape, lysosomal, mitochondrial, % nucleolar, and endosomal channels) .. _demo3D02: demo3D02 -------- Demo header:: % Generate surface plot of image synthesized by demo3D00. % % Input % ----- % * three TIFF files (nuclear, cell shape, and nucleolar channels) % from demo3D00 directory % % Output % ------ % * a surface plot of the synthetic image .. _demo3D03: demo3D03 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and vesicular channels % from all vesicular object models (nucleoli, lysosomes, endosomes, and % mitochondria) with sampling method set to sample vesicular objects from % Gaussians at density 75 without convolution. The model was trained from % the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * six TIFF files (nuclear, cell shape, nucleolar, lysosomal, endosomal, % and mitochondrial channels) .. figure:: ../images/demo3D03/cell1_ch3.jpg :align: center .. _demo3D04: demo3D04 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and vesicular channels % from all vesicular object models (nucleoli, lysosomes, endosomes, and % mitochondria) with sampling method set to sample vesicular objects from % Gaussians at density 75 without convolution. The model was trained from % the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * six TIFF files (nuclear, cell shape, nucleolar, lysosomal, endosomal, % and mitochondrial channels) .. _demo3D05: demo3D05 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and vesicular channels % from all vesicular object models (nucleoli, lysosomes, endosomes, and % mitochondria) with sampling method set to sample vesicular objects from % Gaussians at density 75 without convolution. The model was trained from % the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * six TIFF files (nuclear, cell shape, nucleolar, lysosomal, endosomal, % and mitochondrial channels) .. _demo3D06: demo3D06 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and protein channels % from all object models (nucleoli, lysosomes, endosomes, mitochondria, and % microtubules) with sampling method set to render vesicular objects as % ellipsoids and convolution with point-spread function. The model was % trained from the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * seven TIFF files (nuclear, cell shape, nucleolar, lysosomal, endosomal, % mitochondrial, and microtubule channels) .. _demo3D07: demo3D07 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and protein channels % from all object models (nucleoli, lysosomes, endosomes, mitochondria, and % microtubules) with sampling method set to sample vesicular objects from % Gaussians at a density of 25 and convolution with point-spread function. % The model was trained from the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * seven TIFF files (nuclear, cell shape, nucleolar, lysosomal, endosomal, % mitochondrial, and microtubule channels) .. _demo3D08: demo3D08 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and vesicular channels % from all vesicular object models (nucleoli, lysosomes, endosomes, and % mitochondria) with sampling method set to render vesicular objects as % ellipsoids without convolution. The model was trained from the Murphy Lab % 3D HeLa dataset. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * single indexed TIFF file which indexes the six TIFF files (nuclear, % cell shape, nucleolar, lysosomal, endosomal, and mitochondrial channels) .. _demo3D09: demo3D09 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and lysosomal channels % from LAMP2 model with sampling method set to render lysosomes as % ellipsoids without convolution. Also render 2D mean projections along XY, % XZ, and YZ axes of image. The model was trained from the Murphy Lab 3D % HeLa dataset. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * three TIFF files (nuclear, cell shape, and lysosomal channels) % * one projection TIFF file % * one projection PNG file .. _demo3D10: demo3D10 --------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and lysosomal channels % with object files that can be imported to Blender from LAMP2 model, % with sampling method set to render lysosomes as ellipsoids without % convolution. The model was trained from the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * three TIFF files (nuclear, cell shape, and lysosomal channels) % * three Wavefront OBJ files (nuclear, cell shape, and lysosomal channels) .. figure:: ../images/demo3D10/blender.png :align: center .. _demo3D11: demo3D11 -------- Demo header:: % Train 3D generative model of the cell framework (nucleus and cell shape) % using the Murphy Lab 3D HeLa TfR dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid model .. _demo3D12: demo3D12 -------- Demo header:: % Train 3D generative model of the nucleus, cell shape, and lysosome using % 30 LAMP2 images in the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo3D13: demo3D13 -------- Demo header:: % Export images synthesized by demo3D01 as object files importable to % Blender. % % Input % ----- % * a directory of 3D synthetic images % % Output % ------ % * Wavefront OBJ files .. _demo3D14: demo3D14 -------- Demo header:: % Render 2D mean projections along XY, XZ, and YZ axes of images % synthesized by demo3D00. % % Input % ----- % * a directory of 3D synthetic images % % Output % ------ % * projections of synthetic images as TIFF files .. _demo3D15: demo3D15 -------- Demo header:: % Synthesize one multichannel 3D image from an endosomal model and % diffeomorphic nuclear and cell shape model. The sampling method was set % to render endosomes as ellipsoids without convolution. The model was % trained from the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a valid CellOrganizer model file with a diffeomorphic framework % % Output % ------ % * three TIFF files (nuclear, cell shape, and endosomal channels) .. _demo3D16: demo3D16 -------- Demo header:: % The main idea behind this demo is to show the user they % can use their own binary images from raw experimental data % to synthesize protein patterns. This demo uses the CellOrganizer % method for nuclear and cell segmentation. % % The current demo assumes the resolution of the images is the same as % the resolution of the images that were used to train the protein model. % % Input % ----- % * raw or synthetic images of the nuclear and cell membrane % * a valid CellOrganizer model file % % Output % ------ % * three TIFF files (cell shape, nuclear, and lysosomal channels) .. _demo3D17: demo3D17 -------- Demo header:: % The main idea behind this demo is to show the user they % can use their own binary images from raw experimental data % to synthesize protein patterns. % % The current demo assumes the resolution of the images is the same % as the resolution of the images that were used to train the protein model. % % Input % ----- % * an existing raw or synthetic framework, i.e. one binary multi-TIFF % file of the nuclear channel and one binary multi-TIFF file of the % cell membrane % * the resolution of the latter images % * a valid CellOrganizer model that contains a protein model % % Output % ------ % * three TIFF files (cell shape, nuclear, and lysosomal channels) .. _demo3D18: demo3D18 -------- Demo header:: % Train 3D generative model of the cell framework (nucleus and cell shape), % using hole-finding to infer both nucleus and cell shape from the supplied % protein pattern. The 3D 3T3 dataset was collected in collaboration with % Dr. Jonathan Jarvik and Dr. Peter Berget. % % Input % ----- % * a directory of raw or synthetic protein images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model .. _demo3D19: demo3D19 -------- Demo header:: % This demo uses slml2report to compare the parameters between % CellOrganizer models and returns a report. % % Input % ----- % * a set of valid CellOrganizer models % % Output % ------ % * a report .. _demo3D20: demo3D20 -------- Demo header:: % Train 3D generative diffeomorphic model of the cell framework (nucleus % and cell shape) using 10 images Murphy Lab 3D HeLa LAMP2 dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------- % * a valid SLML model file % * a visualization of the shape space .. _demo3D21: demo3D21 -------- Demo header:: % Train 3D generative model of the cell framework (nucleus and cell shape), % using hole-finding to infer both nucleus and cell shape from the supplied % protein pattern. This is identical to demo3D18 minus scaling the % images. The 3D 3T3 dataset was collected in collaboration with Dr. % Jonathan Jarvik and Peter Berget. % % Input % ----- % * a directory of raw or synthetic protein images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model .. _demo3D22: demo3D22 -------- Demo header:: % Synthesizes a protein pattern instance from the synthetic image produced % in demo3D00. % % Input % ----- % * a synthetic framework % % Output % ------ % * a synthetic image .. _demo3D23: demo3D23 -------- Demo header:: % Train 3D generative diffeomorphic nuclear, cell shape, and a % lysosomal model from all LAMP2 images in the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo3D24: demo3D24 ---------- Demo header:: % This demo converts a sample SBML file to an SBML-spatial instance using % the "matchSBML" function. This function takes an SBML file, matches the % compartments in the file with available models and synthesizes the % appropriate instances. % % Input % ----- % * sample SBML file % % Output % ------ % * valid SBML model .. _demo3D25: demo3D25 ---------- Demo header:: % Synthesizes 1 image using a lysosomal model with sampling mode % set to 'disc', no convolution and output.SBML set to true. % Results will be three TIFF files, one each for cell boundary, % nuclear boundary, and lysosomes, in folder "synthesizedImages/cell1" % Additionally, in the folder "synthesizedImages/" will be a % SBML-Spatial(v0.82a) formatted .xml file containing constructed solid % geometry(CSG) primitives for lysosomes and parametric objects for the % cell and nuclear shapes. % % These files can then be read into VCell using the built in importer or % CellBlender using the helper function provided in this distribution. % % Input % ----- % * valid SBML model % % Output % ------ % * three TIFF files % * XML file with primitives for lysosomes and parametric objects .. _demo3D26: demo3D26 -------- Demo header:: % This function displays a shape space of some dimensionality. This demo % uses the model trained in Johnson 2015. % % Input % ----- % * a CellOrganizer diffeomorphic model % % Output % ------ % * a display of the shape space .. _demo3D27: demo3D27 -------- Demo header:: % This demo performs a regression between two sets of related shapes (i.e. % predicts cell shape from nuclear shape) and displays the residuals as in % Figure 2 of Johnson et al 2015. % % Input % ----- % * models hela_cell_10_15_15.mat and hela_nuc_10_15_15.mat % % Output % ------ % * shape space figure .. _demo3D28: demo3D28 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape, and nucleolar channels % from nucleolar model with sampling method set to render nucleoli as % ellipsoids without convolution. The model was trained from the Murphy Lab % 3D HeLa dataset. % % Input % ----- % * an existing raw or synthetic nuclear image, i.e. one binary multi-TIFF % file of the nuclear channel % * the resolution of the input image % * a valid CellOrganizer model that contains a cell membrane model % % Output % ------ % * three TIFF files (cell shape, nuclear, and nucleolar channels) .. _demo3D29: demo3D29 -------- Demo header:: % Displays information about a model % % Input % ----- % * valid model % % Output % ------ % * details about the models .. _demo3D30: demo3D30 -------- Demo header:: % This demo illustrates how to sample uniformly at random from a % diffeomorphic model. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * a random walk .. _demo3D31: demo3D31 -------- Demo header:: % Trains a generative model of microtubules % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid model .. _demo3D32: demo3D32 -------- Demo header:: % Synthesizes 1 image using a lysosomal model with sampling mode % set to 'disc', no convolution using the object avoidance methods % Results will be three TIFF files, one each for cell boundary, % nuclear boundary, and lysosomes, in folder "synthesizedImages/cell1". % % Input % ----- % * valid SBML file % % Output % ------ % * three TIFF files .. _demo3D33: demo3D33 -------- Demo header:: % Synthesize multiple 3D images from a lysosome model, at different resolutions. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------- % * multiple instances of the same cell at different resolutions .. _demo3D34: demo3D34 -------- Demo header:: % Synthesize one 3D image with nuclear, cell shape and a vesicular channel. % This demo exports the synthetic image as an OME.TIFF as well as an % SBML Spatial instance. % % Input % ----- % * a valid CellOrganizer model % % Output % ------ % * OME.TIFF % * SBML instance % * single channel TIF files .. _demo3D35: demo3D35 -------- Demo header:: % This demo uses slml2model to display information from a valid model file % % Input % ----- % * a valid CellOrganizer model % % Output % ------ % * a report Demo output: .. figure:: ../images/demo3D35/report.png :target: ../_images/demo3D35/report.png :align: center .. _demo3D36: demo3D36 -------- Demo header:: % Synthesize multiple 3D images from a lysosome model at different resolutions. % % Input % ----- % * valid lysosomal model % % Output % ------ % * multiple 3D images at different resolutions .. _demo3D37: demo3D37 -------- Demo header:: % This demo exists to illustrate how padding size and window size affect the % performance of diffeomorphic metric. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------- % * a valid SLML model file .. _demo3D38: demo3D38 -------- Demo header:: % Synthesizes 1 image using a lysosomal model with sampling mode % set to 'disc', no convolution using the object avoidance methods % Results will be three TIFF files, one each for cell boundary, % nuclear boundary, and lysosomes, in folder "synthesizedImages/cell1". % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * three TIFF files (nuclear, cell shape, and nucleolar channels) .. _demo3D39: demo3D39 -------- Demo header:: % This demo illustrates how to sample uniformly at random from a % diffeomorphic model. % % Input % ----- % * a valid CellOrganizer model file % % Output % ------ % * a random walk .. _demo3D40: demo3D40 -------- Demo header:: % Train 3D generative framework model from all LAMP2 images in the Murphy Lab 3D HeLa dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo3D41: demo3D41 -------- Demo header:: % Train 3D generative model of the nucleus, cell shape, and lysosome from % all LAMP2 images in the Murphy Lab 3D HeLa dataset that are either in the % current directory or in the demo3D11 directory. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * a directory of raw or synthetic lysosome images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid SLML model file .. _demo3D42: demo3D42 -------- Demo header:: % This demo illustrates using CellOrganizer to train a protein distribution % model following the approach described in % % K. T. Roybal, T. E. Buck, X. Ruan, B. H. Cho, D. J. Clark, R. Ambler, % H. M. Tunbridge, J. Zhang, P. Verkade, C. Wülfing, and R. F. Murphy (2016) % Computational spatiotemporal analysis identifies WAVE2 and Cofilin as % joint regulators of costimulation-mediated T cell actin dynamics. % Science Signaling 9:rs3. doi: 10.1126/scisignal.aad4149. % % The slowest step, which typically takes about 1 min per cell per frame, % is to align each cell at each time to the standardized template. % This demo uses 46 cells so it will take about 1 hour on a single core. % % Input % ----- % * image and annotation files for one or more proteins for one or more % time points % > the default is to use images from the paper of LAT at time 0 - downloading the % needed images requires about 4 GB of free disk space % % Output % ------ % * a model for the average concentration in each voxel of a standardized % cell shape (in demos/LAT_reltime_1.mat) % * various intermediate results files (in /param and /tmp) .. _demo3D43: demo3D43 -------- Demo header:: % This is the synthesis demo for T cell model. % The demo takes in two models: one model contains both cell and nuclear % shape models, and the other contains a T cell protein shape model. Same % as other synthesis framework, it calls slml2img for the synthesis. The % meanings of the options are commented in the script. % % Input % ----- % * A protein model with type standardized map halp-elipsoid % * A framework model the provide the shape of the cell. % % Output % ------ % * one or more set(s) of synthesized images with cell shape and protein % pattern. .. _demo3D44: demo3D44 -------- Demo header:: % Synthesize a cell shape image from a given constructive_geometry model, % specifically a half-ellipsoid model. % % Input % ----- % * a list of valid CellOrganizer half-ellipsoid model files % % Output % ------ % * a 3D stacked TIFF file Demo output: .. figure:: ../images/demo3D44/image.png :target: ../_images/demo3D44/image.png :align: center .. _demo3D45: demo3D45 -------- Demo header:: % Train 3D generative model of the cell framework (nucleus and cell shape) % using the Murphy Lab 3D HeLa TfR dataset. % % Input % ----- % * a directory of raw or synthetic nucleus images % * a directory of raw or synthetic cell shape images % * the resolution of the images (all images should have the same % resolution) % % Output % ------ % * a valid model .. _demo3D46: demo3D46 -------- Demo header:: % This is the synthesis demo for T cell model. % The demo takes in two models: one model contains both cell and nuclear % shape models, and the other contains a T cell protein shape model. Same % as other synthesis framework, it calls slml2img for the synthesis. The % meanings of the options are commented in the script. % % Input % ----- % * A protein model with type standardized map halp-elipsoid % * A framework model the provide the shape of the cell. % % Output % ------ % * one or more set(s) of synthesized images with cell shape and protein % pattern. Demo output: .. figure:: ../images/demo3D46/image.png :target: ../_images/demo3D46/image.png :align: center .. _demo3D47: demo3D47 -------- Demo header:: % Combine two generative model files into a single file. % % Input % ----- % * a list of valid CellOrganizer model files % % Output % ------ % * a valid model