# u-Signal3D
## User Guide to the u-Signal3D Software Package
![Alt Text](doc/FigUserGuide.png?raw=true)
### Publication
The mathematical approach of the u-signal3D package is described in this paper, [**Cellular harmonics for the morphology-invariant analysis of molecular organization at the cell surface**](https://doi.org/10.1038/s43588-023-00512-4), *Nature Computational Science*, 2023, written by Hanieh Mazloom-Farsibaf, Qiongjing Zou, Rebecca Hsieh, [Gaudenz Danuser](https://www.danuserlab-utsw.org/), Meghan Driscoll.
### Overview
The u-signal3D package is primarily designed to quantitatively analyze the spatial scales of molecular organization at 3D cell surface. We applied the Laplace-Beltrami operator (LBO) to a triangle mesh, represented the cell shape, to generate frequency-based hierarchical functions as a basis function, then decompose cell surface signaling across spatial scales created within this basis set. The u-signal3D framework is a series of MATLAB functions bundled into a user-friendly interface.
### Memory usage
To run the examples, we used a system with 128 GB of RAM. The package can be downloaded and run easily on Windows and Linux. If a lower RAM is used, we recommend monitoring the memory usage. When computing the Laplacian, you can reduce the memory usage by choosing a lower number of eigenvectors ( < 500). This package can run in parallel mode if sufficient memory is available.
### Repository Structure
The u-signal3D package is based on an object-oriented framework developed and used in Gaudenz Danuser’s laboratory. Each data is associated with a MovieData object, which is used to link raw data with analysis outputs. The u-signal3D package includes six processes associated with MovieData objects. The processes are interdependent and run in serial (see example 1).
An alternative approach to the object-oriented format of the package is to use the basic functions associated with each process independently and save the results of each process in the local path. Functions that accumulate data from multiple cells, such as during validation, occur outside of the package framework.
The u-signal3D package accepts 3D images as input. Since the LBO generates the harmonic functions on a triangle mesh, the pipeline includes the cell surface segmentation functionality of an updated version of [u-shape3D](https://github.com/DanuserLab/u-shape3D), which generates surface meshes from 3D images. Users can also import mesh files directly in .obj or .ply format (see example 2). The output of the package is an “energy density spectra”, which describes the spatial scale of molecular organization at the cell surface. The Laplace-Beltrami operator is a scale invariant operator. Thus to measure actual spatial scales, the user needs to generate polka dot patterns on the same cell shape and compare the energy density spectra of the polka dots with the real signal on the same cell surface (see example 3).
The package comprises the following processes,
1. deconvolution – optionally deconvolves the movie
2. computeMIP - optionally generates maximum intensity projections of the movie
3. mesh – creates a triangle mesh representing the cell surface
4. intensity - measures fluorescence intensity near the surface
5. laplacian – computes the Laplace-Beltrami operator harmonic basis functions
6. energy spectra - calculates the energy spectra of surface molecular organization
### Getting Started
1. Download the [code](https://github.com/DanuserLab/u-signal3D/tree/master) and [example image](https://cloud.biohpc.swmed.edu/index.php/s/MfgQ23KWYED66iR/download). Set MATLAB’s path to include all the MATLAB functions provided by this package, using the “Set Path” button in MATLAB (Home > Environment > Set Path > Add with subfolders).
2. To generate polka dot pattern, some mex functions from the toolbox_fast_marching are needed. Before running the code, type these commands in the Command Window:(make sure the package is in MATLAB's current folder)
a. `cd u-signal3D-master`
b. `cd extern`
c. `compile_mex`
d. If done, this message will be shown in the Command Window “MEX completed successfully”
3. To run the Laplacian for non-manifold meshes (not necessary for provided examples), the LBMode should set to‘tuftedMesh’. We wrote a function to use the [non-manifold Laplacian toolbox](https://github.com/nmwsharp/nonmanifold-laplacian). User needs to add the path of two executable files (tufted and tufted-idt) from the Laplace-Beltrami folder into the PATH environment variable of the current system. Please check [README](https://github.com/DanuserLab/u-signal3D/tree/master/nonmanifold-laplacians/README.md).
**Example 1: Spectral decomposition of a molecular signal at the cell surface from a 3D image using the u-signal3D package.**
This example shows how to apply the Laplace-Beltrami operator to a 3D image and generate the energy spectra of molecular fluorescence intensity near the cell membrane.
1. Open [*runUSignal3Dimage3D.m*](https://github.com/DanuserLab/u-signal3D/tree/master/scripts/runUSignal3Dimage3D.m), the script that analyzes the PI3K-labeled cell (Example1), by typing `edit runUSignal3Dimage3D` in MATLAB’s command window.
2. In the set directories section of the m-file, set the paths for
a. imageDirectory – the directory of the provided PI3K-labeled cell
b. psfDirectory – the directory of the provided PSF
c. saveDirectory – the directory where output data will be saved
3. Save the m-file and run it by typing `runUSignal3Dimage3D` in MATLAB’s command window. Note that a pool for parallel processing will likely open. You can control the parallel processing before running the m-file through MATLAB/home/Preferences/Parallel Computing Toolbox.
4. Users can change the parameters for each step (check runUSignal3Dimage3D.m).
Expected output is a folder created in saveDirectory, including a subfolder for each process. The package creates three figures, 1) mesh curvature at the cell surface, 2) intensity of the molecular pattern at the surface, 3) energy spectrum of the molecular pattern.
Running time on a system with 128 GB of RAM: ~ 5 minutes
**Example 2: Spectral decomposition of a molecular signal at the cell surface from a mesh provided as a .obj file.**
This example shows how to apply the Laplace-Beltrami operator to a 3D mesh and generate the energy spectra of molecular fluorescence intensity near the cell membrane (the 3D image is still required to measure the intensity on the mesh surface).
1. Open [*runUSignal3DmeshSurface.m*](https://github.com/DanuserLab/u-signal3D/blob/master/scripts/runUSignal3DmeshSurface.m), the script that analyzes the PI3K-labeled cell (Example2), by typing `edit runUSignal3DmeshSurface` in MATLAB’s command window.
2. In the set directories section of the m-file, set the paths for
a. imageDirectory – the directory of the provided PI3K-labeled cell
b. meshName – the name of the provided mesh (.obj or .ply file) in imageDirectory
c. saveDirectory – the directory where output data will be saved
3. Save the m-file and run it by typing `runUSignal3DmeshSurface` in MATLAB’s command window. Note that a pool for parallel processing will likely open. You can control the parallel processing before running the m-file through MATLAB/home/Preferences/Parallel Computing Toolbox.
4. Users can change the parameters for each step (check runUSignal3DmeshSurface.m).
Expected output is a folder created in saveDirectory, including a subfolder for each process. The package creates three figures, 1) mesh curvature at the cell surface, 2) intensity of the molecular pattern at the surface, 3) energy spectrum of the molecular pattern.
Running time on a system with 128 GB of RAM: ~ 5 minutes
**Example 3: Generating polka dot patterns on a given cell surface.**
This example shows how to generate polka dot patterns on a
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计算平台 u-signal3D 定义了细胞表面分子组织空间尺度的形状不变表示matlab代码.zip (609个子文件)
ply.c 87KB
eucdist2.c 9KB
plytest.c 8KB
use.c 2KB
fibtest.c 2KB
fibtest2.c 2KB
tt.c 1KB
plyfile.cpp 69KB
GW_Parameterization.cpp 49KB
GW_VoronoiMesh.cpp 48KB
GW_Mesh.cpp 29KB
trackball.cpp 19KB
GW_Vertex.cpp 18KB
GW_Toolkit.cpp 17KB
GW_TriangularInterpolation_Cubic.cpp 15KB
GW_BasicDisplayer.cpp 14KB
GW_GeodesicDisplayer.cpp 14KB
fib.cpp 12KB
skeleton.cpp 12KB
GW_GeodesicPath.cpp 12KB
GW_PLYLoader.cpp 11KB
perform_front_propagation_3d - copie.cpp 11KB
GW_ASELoader.cpp 10KB
GW_TriangularInterpolation_Quadratic.cpp 9KB
perform_front_propagation_2d.cpp 9KB
GW_GeometryAtlas.cpp 9KB
perform_front_propagation_3d.cpp 9KB
perform_front_propagation_2d.cpp 9KB
perform_front_propagation_3d_old.cpp 8KB
perform_front_propagation_mesh.cpp 7KB
GW_VertexIterator.cpp 6KB
GW_OBJLoader.cpp 6KB
GW_GeodesicMesh.cpp 5KB
GW_VRMLLoader.cpp 5KB
GW_GeodesicVertex.cpp 5KB
GW_FaceIterator.cpp 4KB
GW_OFFLoader.cpp 4KB
GW_GeodesicFace.cpp 4KB
fm2dAniso.cpp 4KB
GW_TriangularInterpolation_Linear.cpp 4KB
perform_front_propagation_3d_mex.cpp 3KB
perform_front_propagation_2d_mex.cpp 3KB
GW_VoronoiVertex.cpp 3KB
perform_circular_front_propagation_2d.cpp 3KB
perform_front_propagation_anisotropic.cpp 3KB
perform_front_propagation_anisotropic.cpp 2KB
GW_SmartCounter.cpp 2KB
GW_Face.cpp 2KB
GW_GeometryCell.cpp 2KB
GW_InputOutput.cpp 2KB
GW_GeodesicPoint.cpp 2KB
main.cpp 1KB
GW_Config.cpp 1KB
stdafx.cpp 203B
stdafx.cpp 203B
stdafx.cpp 203B
GW_TriangularInterpolation.cpp 14B
perform_circular_front_propagation_2d.def 72B
perform_front_propagation_mesh.def 65B
perform_front_propagation_2d.def 63B
perform_front_propagation_3d.def 63B
mesh3DProcessGUI.fig 91KB
packageGUI.fig 80KB
Intensity3DProcessGUI.fig 54KB
imageDataGUI.fig 52KB
deconvolution3DProcessGUI.fig 51KB
addROIGUI.fig 47KB
movieDataGUI.fig 46KB
movieSelectorGUI.fig 45KB
cropMovieGUI.fig 36KB
imFolderGUI.fig 36KB
channelGUI.fig 33KB
omeroDataSelectionGUI.fig 13KB
omeroLoginGUI.fig 12KB
dataPreparationGUI.fig 9KB
noSettingsProcessGUI.fig 5KB
recycleProcessGUI.fig 4KB
msgboxGUI.fig 2KB
jama_eig.h 29KB
GW_MatrixStatic.h 28KB
GW_MatrixNxP.h 24KB
GW_Matrix4x4.h 19KB
fm2dAniso.h 18KB
GW_Maths.h 17KB
GW_Quaternion.h 16KB
jama_svd.h 15KB
GW_PolygonIntersector.h 14KB
GW_VectorND.h 13KB
GW_Config.h 13KB
GW_SparseMatrix.h 13KB
GW_VectorStatic.h 12KB
GW_Matrix3x3.h 12KB
tnt_cmat.h 11KB
GW_MathsConfig.h 11KB
GW_Parameterization.h 10KB
tnt_array3d.h 10KB
tnt_array2d.h 10KB
tnt_array1d.h 9KB
GW_VoronoiMesh.h 9KB
tnt_fortran_array3d.h 9KB
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