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1. 50 TES YES 50 TES YES TES YES skeleton YES YES stomach TES YES Cancel Figure 11 Display Properties Setting Figure 12 Display properties renderings Window Window Help Cascade Tile Arrange Icons Set the view s layout Cascade View cascade Tile View tile Arrange Icons Arrange Icons Help About Mose Help Files About MOSE Display the version and copyright information of MOSE Help Files Show the help file of MOSE 2 2 1 2 Tool Bar The toolbar is a series of function button combination which provides a shortcut method to perform common commands Table 1 Description of the toolbar Icon Function Open project Led Save parameters results m e Unfold Fold sidebar R By roscoe gt Start simulation lL J e sosm Show Hide colorbar E Bie 2 2 1 3 Side Bar The sidebar is another interface to input parameters It remains the style of the input parameter interface including four sub pages medium light source detector and simulation property The steps of modification of the parameters are the same as the parameter setting dialog on the menu bar See chapter 2 2 2 e Medium page The upper part of the window shows the names of the tissues and the lower part shows the shape parameters The shape can be divided into two types regular and irregular As shown in Figure 13 If regular the lower part shows the center and the axis lengths of the shape
2. favelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refractive Index Apply Figure 21 Main interface of the parameter setting Parameter File Input Click Load File Import simulation parameter file from external shown as Figure 22 MOSE sets a fixed format for the parameter file users need to set the parameter file according to the file format requirements Specific parameter file format see Chapter 3 After loading the parameter file users can still modify the parameters in the Parameter Setting dialog box 3D Parameter Setting Light Source Detector Simulation Property Tissue with Regular Shape Tissue Name Tissue Index Outermost Tissue B bl tCylinder mse ses w seat Wavelengh mm Absorption 1 mm Scattering 1 mm Anisotropy Refractive Index Figure 22 Interface of choosing parameter file Dialog Box Input User can also set various simulation parameters through the dialog box interface The functions of various buttons on each sub page are described below including 5 parts the main interface of parameter setting the medium interface the light source interface the detector interface and the interface of simulation properties 1 Main Interface of Parameter Setting Click Add spectrum uses can add a new spectrum as shown in Fig 23 Due to the different optical parameters among different spectrums users should enter the optical parameters of the tissues a
3. CountR CountA The numbers of data along radial direction and azimuth angle direction respectively 3DCWTransmittanceBottomRA The transmittance results on the bottom 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 20 Format of the transmittance results for the shape of cylinder in Cartesian coordinate system under CW 3DCWTransmittanceSide The total transmittance on the side of the cylinder CountA CountZ The numbers of data along azimuth angle direction and Z axis respectively 3DCW TransmittanceSideAZ The transmittance results on the side 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceTop The total transmittance on the top of the cylinder CountX CountY The numbers of data along X axis and Y axis respectively 3DCWTransmittanceTopX Y The transmittance results on the top 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceBottom The total transmittance on the bottom of the cylinder CountX CountY The numbers of data along X axis and Z axis respectively 3DCWTransmittanceBottomX Y The transmittance results on the bottom 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 Table 21 Format of the transmittance results for the shape of cube under CW
4. Output Graph CW Transmittance BrE Background Color Color Bar Render Method skin Perspective Projection heart Y Orthographic Projection liver Viewing Options lungs stomach Parameter Data path D Abj_ply bj_aitt Face number 50000 Medium Gi eht Figure 9 Orthographic Projection Show Photon Trajectory Set whether show photon running path in the process of simulation or not After setting the view will display the path of each photon running However this will largely reduce the simulation speed Do not suggest users set this item The effect is displayed in Figure 10 Hose mewpro 3D Parameter Map File Input Qutput Simulation View Window Help a A l b o e o a e Output Graph Select Spectrum Light source 1 Part 1 2 Optical simulation in medium 17 7 _ Execute Time 0 d 00 h01 m36s Parameter Data shape ELLIPSOID v HT center x mm 25 center y mm center z mm a mm b mm c mm AzimuthalAngleMin AzimuthalAngleM DeflectAngleMin DeflectAngleMax Internal Solid Specular Figure 10 Show Photon Trajectory Viewing Options Set display properties of the medium the light source and the detector in different types of map parameter map absorption map transmittance map They include Color Opacity Show Hide and Solid Wireframe as shown in Figures 11 12 Color Property in Original Map Medium Light Source Detector 20 TES YES
5. anisotropy factor and refractive index As shown in Figure 25 the first list in the medium interface displays the parameters of the tissues with regular shapes the second list in the medium interface displays the parameters of tissues with irregular shapes and the last list in the medium interface displays the optical parameters of the tissue chosen by users 3D Parameter Setting Medium Light Source Detector Simulation Property Load File Tissue with Regular Shape Tissue Name Outermost Add Spectrum Del Spectrum lt M Tissue with Irregular Shape Triangle Mesh Tissue Name Outermost Shape File Path Change Path PhantomSur face YES D MOSE v2 1 2beta use_skin_10000 off Browse HO D MOSE v2 1 2beta usc_skeleton_25000 off Browse Optical Parameter of PhantomSurface favelengh am Absorption 1 mm Scattering 1 mm Anisotropy Refractive Index 0 050000 10 000000 0 900000 1 300000 Figure 25 Interface of setting the tissue parameters Table 2 Description of the parameters of the tissue with regular shape The name of the tissue The number of the tissue in the tissue list of the medium Outermost Outermost flag The flag is Yes if the tissue is the outermost one in the tissue list of the medium The outermost tissue has the largest bounding box and other tissues are inside of it In the parameter setting of the medium the outermost tissue must be only one otherwise the sim
6. 2D Polar Cartesian 3D Cartesian Cylindrical to save the absorption results The raw Absorption absorption results photon density can be processed to the photon fluence users need to choose one type between photon density and photon fluence Setting of the coordinate system The type of the coordinate system is correlated to the shape of the medium Currently the Transmittance type will be modified automatically by the program to avoid the wrong setting Setting of the separations in ROI along different directions Separation including X axis Y axis Z axis radius azimuth angle deflection angle and time please refer to Figure 65 in Section 3 2 2 Setting of the minimums of ROI 7 Maximum Setting of the maximums of ROL Frequency MHZ The modulating frequency under FD the unit is MHZ Users will enter the interface of the optical simulation shown in Figure 36 after finishing the parameter setting and clicking OK in the main interface of parameter setting In the sidebar the parameters completed just now will display which makes it easy for users to modify 2 Hose newpro 3D Parameter Map File Input Qutput Simulation View Window Help E Lay 2 ted lof ey l gt E ke Select Spectrum Output Graph skin heart liver lungs stomach Parameter Data path D bj_ ply bj_attl Face number Yertex number 25001 Bound minX 13 131900 Bound maxX 28 546499 Bound minY 4
7. Simulation View Window Help Hegde Output Graph Select Spectrum Figure 52 Display after setting parameters in 2D 3D energy mapping Click Simulation Start to start the mapping process as shown in Figure 53 Output Graph Select Spectrum 3D Mapping 34 9 Execute Time 0d00h00m01s Figure 53 Running interface of the 2D 3D energy mapping The mapping result after running is shown in Figure 54 2 Mose newpro4 3D Photon Detector Map lt gt File Input Qutput Simulation View Window Help ap y b J gt Bz Oy Output Graph CW Detector Map v Select Spectrum 620 v Detector Num CY Detector Map CW Transmittance Map Figure 54 Display of the detection result 2 Hose newpro4 3D Photon Transmittance Map gt File Input Output Simulation View Window Help HavVveeEae Output Graph CW Transmittance Map Y Select Spectrum 620 v min 0 00e 000 Fig 55 Display of the mapping result on the surface of the medium 2 4 Image Processing Select the type of image processing project and enter its interface This project has two functions threshold extraction and mesh simplification 2 4 1 Threshold Extraction The function of the threshold extraction is to extract the surface within a certain threshold from the RAW date captured by CT MRI and the surface is constructed by triangular mesh For example select File Load Volume RA
8. aes i a The focus of the lens NOTE 1 File header 2 Simulation properties 3 Spectrum list 4 Light source parameters 5 Medium parameters 6 Detector parameters The comment lines started with the symbol Table 14 Difference of the light source properties in different simulation type Forward simulation type a a Luminescence l l l l Eaa E Bioluminescence Incident laser Incident laser Excitation fluorophore Emission type The incident laser can be inside or outside the Inside the Inside or outside the Position medium The fluorophore must be inside the medium medium medium Yes can be set while Specular Yes can be set while the incident laser is outside the incident laser is reflectance the medium outside the medium The spectrum parameters of the incident Including central laser include central wavelength spectrum Including central wavelength energy and photon number Spectrum wavelength spectrum spectrum energy The spectrum parameters of the fluorophore parameters energy and photon and photon include emission wavelength excitation number number wavelength quantum yield absorption factor and fluorescence lifetime 3 2 2 Shape Parameters and ROI Figure 63 Illustration of the parameters of the 3D shapes Point O is the center a b c are the half of the axis length along X axis Y axis and Z axis respectively X Figure 64 Illustration of the parameter
9. detector number in Detector Num 1 the drop down box i the order of the numbers is in accordance with the order of the detectors in the parameter file as shown in Figure 40 max l dJe UHA 11 4 mint Oe Figure 40 Photon detection figure Output CW TD FD Absorption Map To show the photon absorption figures under CW TD and ED respectively There are two ways to show the absorption figure Single Layer and Multilayer The slider controls the display of the specific number of the layer when using single layer display and the dialog box controls when using multilayer display The Figures 41 44 while using Cartesian coordinate system The Figures 45 47 while using Cylindrical coordinate system The detailed description of these dialog boxes are shown in table 10 Absorption Map Setting Single layer Multilayer Single layer Setting Setting Select Spectrum 620 Select Spectrum Plane Setting Plane Setting C xY Plane CO xY Plane Total number 0 Ll Y Z Plane L Y Z Plane Total number 0 Z Plane C1Xx Z Plane Total number 0 Seperate the numbers with space a Single layer display setting b Multilayer display setting Figure 41 Settings of the absorption figure under CW with Cartesian coordinate system Time Domain Absorption Map Setting a Single layer display setting b Multilayer display setting Figure 42 Settings of the absorption figure under TD with Cartesian coordinate system
10. environment Please see Chapter 3 for parameter file format Output Output Simulation Paramter Simulation Parameter Output the simulation parameters used in the current simulation to the constructed project folder the document suffixes is MSE 3D Simulation Result After complete simulation output the simulation results to the constructed project folder including absorption results transmission results and detection results CW Absorption Map Display the photon absorption map under CW CW Transmittance Map Display the photon transmittance map under CW CW CCD Map Display the detection map captured by CCD This function can only be chosen in 3D CW TD Absorption Map Display the photon absorption map under TD TD Transmit Map Display the photon transmittance map under TD FD Absorption Map Display the photon absorption map under FD Amplitude and phase respectively FD Transmit Map Display the photon transmittance map under FD Amplitude and phase respectively Simulation Start Start simulation Stop Stop the simulation during the simulation process the program will return a warning on failure View View Window Help Toolbar w Status Bar Select Plane Backzround Color Color Bar Render Method Projection r F F0 F F Toolbar Set whether display function button bar or not Status Bar Set whether display status bar or not Select Plane Select Pla
11. in Table 15 3DFDAmpTransmittanceMeshFace The amplitude of the transmittance on each mesh face 0 00000e 000 Same as that in Table 15 3DFDPhaTransmittanceMeshFace The phase of the transmittance on each mesh face 0 00000e 000 Same as that in Table 15 CountMesh Vertex Same as that in Table 15 3DFDAmpTransmittanceMesh Vertex The amplitude of the transmittance on each mesh vertex 0 00000e 000 Same as that in Table 15 3DFDPhaTransmittanceMesh Vertex The phase of the transmittance on each mesh vertex 0 00000e 000 Same as that in Table 15 3 3 3 2 Absorption Results Compared to the absorption results under CW the absorption results under FD include amplitude and phase as shown in Table 30 Table 30 Format of the absorption results in 3D Cartesian coordinate system under FD 0 00000e 000 0 00000e 000 Same as that in Table 22 3DFDPhaAbsorptionX YZ The phase of the absorption in 3D Cartesian coordinate system 0 00000e 000 0 00000e 000 Same as that in Table 22 4 Frequently Asked Questions FAQ 1 Can I use MOSE in a commercial organization Yes MOSE is free software You can use it on any computer You just need to register without pay for MOSE 2 Why the display of the parameters doesn t change after modify the parameters through the side bar Users need to click the button Save Parameters Results on the toolbar after modify the parameters through the side bar Then the display will u
12. mctrianglmesh Cartesian FluenceRate The flag of whether to calculate the internal fluence rate based on the photon density Raw absorption There are only one type of data can be saved in each simulation PhotonFlyTime The flag of whether to record the fly time of transmitted photons under TD OutermostTissueIndex The number of the outermost tissue in the tissue list of the medium The outermost tissue has the largest bounding box AmbientMediumR The refractive index of the ambient medium Domain CW The simulation domain 1 CW There are no more parameters need to be set 2 TD In addition to the above parameters needed to be set the parameters related to time need to be set The order is Tmin Tmax and Dt which are corresponding to the minimum time the maximum time and the time interval respectively Unit picosecond FD Under FD users still need to set the modulating frequency Unit MHZ endSimulationProperty a The keywords to end the setting of the simulation property 3 Spectrum Spectrum list the order is spectrum number and the central wavelength of the spectrum Unit nanometer For example Spectrum 1 650 Spectrum 2 690 LightSource The light source parameters and its number LightSourceShape The shape of the light source 1 3D Ellipsoid Cylinder Cube MCTriangleMesh Irregular shape 2 2D Ellipse Rectang
13. need to click toolbar Save Parameter Result to save modified parameters At the same time the view area will update the modified parameters 2 2 1 4 View Area View area is the display area mainly responsible for displaying the simulation parameters and the simulation results As shown in Figure 17 Figure 17 View Area Some operations of view area have been introduced in section of menu bar In addition clicking the right middle and left mouse buttons can realize the rotation move and enlarge reduce operations respectively Simulation parameters map photon absorption map photon transmittance map and photon detection map can be chosen from the output menu or output graph on toolbar As shown in Figure 18 Output graph Parameter Map Parameter Hap CY Absorption Map CY CCD Map CWI Transmittance Mar Figure 18 View area operations 2 2 1 5 Status Bar The main function of the status bar is to display the progress information while saving or reading simulation results As shown in Figure 19 Mose newprol 3D Monte Carlo Simulation lt gt File Input Qutput Simulation View Window Help Ha A l b o A e a a Output Graph v Select Spectrum skin heart liver lungs stomach Loading Project Parameter Data path DAbj_phy bj_atl Face number 50000 Vertex number 25001 Bound minx 13 131900 Bound maxx 28 546499 Bound minY 4 416250 Bound maxY 57 676998 Bound minZ 3 8
14. 0 000000 21 000000 0 000000 0 000000 0 000000 0 000000 Del Spectrum Ka ili Light Source with Irregular Shape Triangle Mesh Shape File Path Change Path Azimuthal Angle min Azimuthal Angle max Deflect i Property of Light Source 1 Wavelengh nm Number of Photons Spectrum Energy Excitation Wavelength nm Quantum Yield 1000000 1 000000 0 0 000000 Add Light Source Del Light Source Figure 29 Interface of setting the light source parameters Table 5 Description of the parameters of the light source with regular shape The number of the light source The shape of the light source Y The central coordinate of the tissue shape along Y axis Z The central coordinate of the tissue shape along Z axis x T a ote ane ote tissue shape alone Xamis Ts Hato exis en oft ave shape lng Yanis Azimuthal Angle Max The maximum of azimuth angle of emitted photon Internal Flag YES means the light source is inside the medium NO means the light source is outside the medium Solid Flag YES means the photon is generated inside the shape or on the boundary of the shape of the light source NO means the photon is generated on the boundary of the shape Specular Flag YES means the specular reflectance will happen while the light source is outside the medium NO means no specular reflectance Luminous Type Luminous type of the light source There are f
15. 30420 Bound maxz 91 900101 Oheim Qrient rete Qsinat Ready oT Figure 19 Status bar 2 2 2 Simulation Example 2 2 2 1 New Project Users need to choose the optical molecular imaging project and space dimension in the New Project page For example Figure 20 shows the interface after users choose the optical molecular imaging project under 3D environment and clicks OK Mose newpro 3D Monte Carlo Simulation d gt File Input Qutput Simulation View Window Help Ha I le A gt Jt Output Graph Select Spectrum Figure 20 Interface of the optical molecular imaging project under 3D environment 2 2 2 2 Input Simulation Parameters Input parameters have the same steps in both 2D and 3D environment Here we only take the 3D environment as an example Select Input 3D Parameter the Parameter settings dialog box is popping up as shown in Figure 21 The dialog box has four different sub pages Medium Light Source Detector Simulation Property There are two ways to set the simulation parameters Parameter file input and dialog box input They are described separately below 3D Parameter Setting Medium _ Light Source Detector Simulation Property _ Tissue with Regular Shape Tissue Name Outermost Add Spectrum Del Spectrum S l _ Tissue with Irregular Shape Triangle Mesh Tissue Name Tissue Index Outermost Shape File Path Change Path Optical Parameter
16. 3DCWTransmittanceTop The total transmittance on the top of the cube CountX CountY The numbers of data along X axis and Y axis respectively 3DCWTransmittanceTopX Y The transmittance results on the top 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceBottom The total transmittance on the bottom of the cube CountX CountY The numbers of data along X axis and Y axis respectively 3DCWTransmittanceBottomX Y The transmittance results on the bottom 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceLeft The total transmittance on the left side of the cube CountX CountZ The numbers of data along X axis and Z axis respectively 3DCWTransmittanceLeftXZ The transmittance results on the left side 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceRight The total transmittance on the right side of the cube CountX CountZ The numbers of data along X axis and Z axis respectively 3DCWTransmittanceRightXZ The transmittance results on the right side 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceFront The total transmittance on the front side of the cube CountY CountZ The numbers of data along Y axis and Z axis respectively 3DCWTransmi
17. 416250 Bound maxY 57 676998 Bound minZ 3 830420 Bound maxZ 91 900101 Qitediun Qi eht Figure 36 Interface after finishing the parameter setting 2 2 2 3 Start Simulation The simulation will start after finishing the parameter setting and clicking Simulation Start in the menu bar or the toolbar as shown in Figure 37 The running time and the percentage are shown in the progress bar which is used for reference C Hose newpro 3D Parameter Kap File Input Qutput Simulation View Window Help E J Ly l Z td lof Ez gt LJ B i Output Graph Select Spectrum skin heart liver lungs stomach Part 1 2 Optical simulation in medium 1 0 Execute Time 0 d 00 h 00 m 22 s L Parameter Data path D bj_ ply bj_attl Face number 50000 Vertex number 25001 Bound minx 13 131900 Bound maxX 28 546499 Bound minY 4 416250 Bound maxY 57 676998 Bound minZ 3 830420 Bound maxZ 91 900101 Qedim QLizht Figure 37 Interface of running the optical simulation Meantime users can click the shortcuts in the toolbar or select Simulation Stop in the menu bar to break off the running and the simulation will end in failure Mose newpro 3D Parameter S ox gt Sle Ne 2vesseeene Output Graph Select Spectrum skin heart liver lungs stomach Parameter Data path D bj_ ply bj_atl Face number 50000 Vertex number 25001 Bound minX 13 131900 Bound maxX 28 546499 Bound
18. D 3D energy mapping as shown in Figure 49 Hew Project Project Name _newpro Project Path Select Project Type Optical Molecular Imaging Forward Simulation of BLT DOT or FMT Simulation Dimension 2D 3D Energy Mapping Image Processing Surface Reconstruction Surface Simplification Figure 49 Building a project of 2D 3D energy mapping The interface is shown in Figure 50 after clicking OK Hose mewpro4 3D Parameter Kap lt gt File Input Output Simulation View Window Help a B a e E ea Output Graph Select Spectrum Figure 50 Interface after building the project of 2D 3D energy mapping Click Input 3D Parameter or Input Parameter on the toolbar the interface of the parameter setting is shown in Figure 51 3D Happing Parameter Parameter cal fHavelength Detector Index Shape File Fath Change Fath 620 1 D mappingfluc Bhmin bin fr Browse Del Detector Result Figure 51 Interface of parameter setting Table 11 Description of the parameters on the interface of parameter setting The path of the parameter file Add Detector Result Add a detection result Del Detector Result Wavelength The central wavelength of the spectrum Detector Index The number of the detector The interface after inputting the parameters is shown in Figure 52 Hose newpro4 3D Parameter Map rts File Input Qutput
19. Frequency Domain Absorption Hap Setting x a Single layer display setting b Multilayer display setting Figure 43 Settings of the absorption figure under FD with Cartesian coordinate system Absorption Map Setting Single layer Multilayer Setting Select Spectrum 620 Plane Setting x Y Plane Y Z Plane X Z Plane 63 107 3 830420 91 900101 Absorption Map Setting Single layer Multilayer O Single layer Setting Setting Select Spectrum 620 Select Spectrum Plane Setting Plane Setting L X Y Plane L X Y Plane Total number 0 C Parallel to Z Axis C Parallel to Z Axis Total number 0 Separate the numbers with space a Single layer display setting b Multilayer display setting Figure 45 Settings of the absorption figure under CW with Cylindrical coordinate system Time Domain Absorption Map Setting fx Time Domain Absorption Map Setting Select the number of time Select the number of time Single layer Setting Setting Select Spectrum 620 Select Spectrum 620 Plane Setting Plane Setting L X Y Plane C X Y Plane Total number 0 Parallel to Z Axis C Parallel to Z Axis Total number 0 Separate the numbers with space a Single layer display setting b Multilayer display setting Figure 46 Settings of the absorption figure under TD with Cylindrical coordinate system Frequency Domain Absorption Map Setting Frequency Domain Absorpti
20. Home Page Molecular Image Group Life Sciences Research Center Xidian University Medical Image Processing Group Institute of Automation Chinese Academy of Sciences Biomedical Imaging Division School of Biomedical Engineering amp Sciences Virginia Tech Wake Forest University USA MOSE Molecular Optical Simulation Environment User Manual Version 2 1 2 Last update 2010 12 24 Ge Wang Ph D wangge vt edu Jie Tian Ph D tian 1eee org Jimin Liang Ph D jimleung mail xidian edu cn Nunu Ren Ph D Candidate rennunu gmail com 1 About MOSE The functions of MOSE and its application areas will be introduced in this chapter Compared to the previous version the new version has made great improvements to meet the requirements of the users 1 1 Introduction Optical molecular imaging using near infrared light is very useful to study the development and changes of disease in the biomedical field Over past twenty years optical molecular imaging has attracted more and more attention and made a series of progress and breakthrough The imaging technologies can be divided into two groups the first is the two dimensional 2D planar imaging and the second is the three dimensional 3D tomographic imaging such as diffuse optical tomography DOT fluorescence molecular tomography FMT and bioluminescence tomography BLT The forward problem of tomographic imaging is to study the light propagation and the inverse pr
21. If irregular the lower part shows the path of the shape file ply off surf mesh the face number the vertex number and the bounding box Users can modify the shape parameters directly Right click the tissue name and we can add tissue delete tissue or modify optical parameters of the tissue in each spectrum x x Pa Pas PhantomSurface skin a bladder J cerebellum we jdd Tissue kidi live lunge pancreas skeleton spleen stomach tetis Del Tissue Optical Farameters Parameter Data Parameter Data path C Documents a shape CUBE st Face number 3500 center x mm Yertex number 1752 center y mm 0 0 Bound minx 14 354100 center z mm 0 0 Bound maxx 23 235500 a mm 20 Bound minr 35 555801 b mm 20 Bound ma r 45 450001 Bound minz 4 950000 c mm 7 0 Bound max 11 050800 a Regular shape b Irregular shape Figure 13 Medium page on sidebar e Light Source Page This page is the same as the Medium page the upper part shows all the numbers of the light sources Click a light source the lower part will show its shape parameters Light source shapes also can be divided into regular and irregular Right click light source and we can add light source delete light source or modify the properties of the light source in each spectrum x iti Light source 1 Add Light Source Del Light Source Property Parameter Data shape muro cent
22. OSE the detailed information will be introduced in the following sections The solution of the inverse problem remains under investigation and will be added in future version 1 2 New Features Compared to the previous version the update provides some new functions and greatly increases the stability and efficiency The main contents are as follows 1 Add the simulation of two types of optical imaging including DOT and FMT 2 Add two domains including TD and FD 3 Add the simulation of light propagation in free space under CW based on the method of pinhole projection 4 Add the function of reverse mapping from the fluence measured by detector to the flux on the boundary of the medium 5 Add the multithreaded simulation which can make the most of the strengths of the multicore CPU 6 Add the function of calculating the photon fluence from the raw absorption photon density 7 Improve the display functions include a Add the function of display setting of the tissues in the medium The setting includes show hide color transparence solid wireframe and so on b Add the function of interpolation while rendering the simulation results c Add the function of multilayer displaying of the absorption results 8 Extend the functions of file input and output include a Add the input output function of the data generated by the different simulations b Support two new file formats including MESH and SURF which are both used to de
23. W IMG file and enter the parameter setting dialog box as shown in Figure 56 The detailed description on the dialog is in the Table 11 Open RAW ING file Information Data type unsigned char 8 bits w Requested 2621 44 bytes Filesize 0 bytes idth Pixel interval Height Pixel interval 1 Number of slice slice interval Number of channels Little Endian Head length Interleaved Storing Figure 56 Dialog box of reading RAW format file Table 12 Description of the parameter setting while reading RAW format file Filename The path of the RAW IMG file Data type The data type of the RAW IMG file Repuested Calculated size of the file according to the input parameters Check the correction of the input parameters by comparing the calculated size to the actual size of the file Filesize The actual size of the RAW IMG format file Width The width of each slice and the size of each pixel Number of channels Channel number 1 Gray image 2 RGB image 3 RGBA image Click OK after finishing the parameter setting The interface likes the Figure 57 if the input data are correct x Oy x lt gt File Mesh Simplification Segmentation View Window Help 2000008 Ready Figure 57 Display after reading RAW format file Select Segmentation Threshold Segmentation it provides a threshold setting dialog box Set the upper and lower threshold and obtain t
24. ameter Map Select Spectrum x 4 newprol 30 Pacameter Bap we akin hear liver lungs homach de perprol 40 Fhoton Trumnamittance Bap tlia ed d neeprol 3J0 Photon Absorption Bap ja a fe Parameter Dala i _ path Cb phythj_ atl Face number soppan MSi Harai ee Veres number 25001 Tar Bound mink 13 131300 Bound mas FES 4bguu Bound min 4 416750 Bound maxr TRTA Ei Bound minz J 030470 Bound ma TANET AN Figure Open a project NOTE Read a larger amount of data may take some time The program state after reading is determined by the last run state of the project For example if only the parameters are inputted in the last run of the project it s required to simulate and output the results If none of the parameters is inputted it s also required to set the parameters If the simulation has done and the results have outputted users can directly observe the results obtained from last run after opening the project this time 2 3 Energy Mapping From 2D to 3D 2 3 1 Function It can build a mapping from 2D photographic images to 3D spatial distribution on the body surface In addition combining with the algorithm of solving the inverse problem based on photon transport model we can reconstruct the spatial distribution of optical properties of the medium or of bioluminescent source inside the medium 2 3 2 Example Click File new or click New Project on the toolbar and select 2
25. and mesh simplification As shown in Figure 1 there are two options including New Project or Open Project can be chosen after MOSE started New Project Build a new project object as shown in Figure 2 The purpose of build project is to facilitate unified management of the data that related to the simulation Each individual project is corresponding to a separate folder Project name and project path are set freely by users After click OK a project folder in the project path will be generated The folder contains a project file suffix mpj Please do not modify the project file to avoid unknown error Open Project Open an existing project object including various data generated by the simulation As shown in Figure 3 SS Hose F m x File View Help Figure Start MOSE Hew Project oj Pt Select Project Type Optical Molecular Imaging Forward Simulation of BLT DOT or FMT Simulation Dimension 2D 3D 2D 3D Energy Mapping Image Processing Surface Reconstruction Surface Simplification Figure 2 Build a new project Hose newpro 3D Monte Carlo Simulation lt File Input Output Simulation View Window Help H Bbk ae ene Output Graph Parameter Map v Select Spectrum MouseSurface Loading Project Parameter Data shape CYLINDER center x mm center y mm center z mm a mm b mm 10 0 Medium Qriat Orete Osima L
26. ence in FMT Absorption Factor The absorption factor of the fluorescence in FMT The life time of the fluorescence in FMT Click Add Light Source the selection dialog box Shape Type pops up as shown in Figure 30 Click Del Light Source the optical parameters of the light source selected in the list will be deleted Shape Type Triangle Mesh off ply surf mesh Figure 26 Selection dialog box of the light source shape After selecting the shape users will enter the interface shown in Figure 31 or 32 Fig 27 shows the adding interface of the light source with regular shape corresponding to Tables 5 and 7 Fig 32 shows the adding interface of the light source with irregular shape corresponding to Tables 6 and 7 Add Light Source Light Source Parameter Shape Ellipsoid v Luminous Type BLT Center Position mm Half Axis mm Internal Solid Specular Photon Emitting Azimuthal Angle Deflect Angle Min 0 degree Min 0 degree Max 360 degree Max i degree Property Wavelength nm Number Of Photons Spectrum Energy Excitation Wav G Figure 31 Dialog box of adding light source with regular shape Add Light Source Light Source Parameter ricpats a a amine te Photon Emitting Azimuthal Angle Deflect Angle Internal YES Min Solid ES eo Specular Property Wavelength n
27. er spectrum energy photon number Fluorophore the order is spectrum number excitation wavelength quantum yield absorption factor fluorescence lifetime 0 360 LightSourceAzimuthalang The range of the azimuth angle of the emitted photon The le maximum range is 0 360 LightSourceDeflectAngle 0 180 The range of the deflection angle of the emitted photon The maximum range is 0 180 The tissue parameters and its number Set the shape of the tissue The center of the shape Half of the axis length of the shape see Figures 63 64 for more TissueShape TissueAxis information TissuePath The path of the triangle mesh file used to describe the irregular shape TissueSpectrumIndex The optical parameters of the tissue The order is spectrum Bese number absorption coefficient scattering coefficient anisotropy factor refractive index DetectorLens VerticalPlane XY The plane of the detector perpendicular to including XY YZ ZX NOTE The structure design of the detector in MOSE is The detector parameters and its number shown in Figures 66 68 DetectorNormal DetectorSize The center of the detector The normal vector of the detector The actual size of the detector the order is height width DetectorResolution The resolution of the detector the order is height resolution width resolution ImageDist The image distance of the detector
28. er x mm center Yy mm 60 0 center z mm 14 0 a mm 0 0 b mm 0 0 c mm 0 0 AzimuthalAngleMin 0 0 AzimuthalAngleM 360 0 Deflect4ngleMin 0 0 DeflectAngleMax 160 0 Internal Solid Specular Medium Li ght Figure 14 Light source page on sidebar e Detector Page The upper part shows all the numbers of the detectors Click a detector the lower part shows the parameters of the detector Users can modify the detector parameters Right click a detector and we can add detector delete detector x gt Z Add CCI Tel CCI Parameter Data Yertical Plane ee Center x Center r 0 0 Center Z 0 0 Normal 0 0 Normal r 0 0 Normal Z 1 0 Focal Length 55 0 Image Distance 72 5403 Detector YYidth 13 8 Detector Height 13 8 Width Resolution 126 Height Resolution 128 Lens Radius 1 0 Q Medium GLi eht Dete Figure 15 Detector page on sidebar e Simulation Property Page This page shows the simulation type absorption matrix transmittance matrix region of interest and so on Type of Forward Simulation BLT OFMT ODOT Domain M CW ITD C FD Medium Algorithm Type VRMC ka Freespace Algorithm Type PINHOL w ROI Absorption Cartesian Transmittance Cartesian v Separation R jii Angle degree Time 0 100000 PS O Minimum Maximum x ma pes vi pa srr z ps is a 0 0 oo Figure 16 Simulation properties page on sidebar NOTE After modified users
29. esh under TD 3DTDTransmittanceMesh The total transmittance on the triangle meshes in the first time segment CountMeshFace Same as that in Table 15 3DTDTransmittanceMeshFace The transmittance results on each mesh face in the first time segment 0 00000e 000 Same as that in Table 15 CountMesh Vertex Same as that in Table 15 3DTDTransmittanceMesh Vertex The transmittance results on each mesh vertex in the first time segment 0 00000e 000 Same as that in Table 15 The total transmittance in the second time segment 0 00000e 000 0 00000e 000 NOTE The contents in red font are the difference from that in Table 15 3 3 2 2 Absorption Results Compared to the absorption results under CW the absorption results under TD just increase the time as shown in Table 28 Table 28 Format of the absorption results in 3D Cartesian coordinate system under TD 0 00000e 000 0 00000e 000 Same as that in Table 22 The total absorption in the second time segment 3DTDAbsorptionX YZ Same as that in Table 22 0 00000e 000 0 00000e 000 Same as that in Table 22 3 3 3 FD 3 3 3 1 Transmittance Results Compared to the transmittance results under CW the transmittance results under FD include amplitude and phase as shown in Table 29 Table 29 Format of the transmittance results for the shape of triangle mesh under TD Content Explanation Domain FD The simulation domain CountMeshFace Same as that
30. folder 3 Description of the File Format in MOSE This chapter will focus on the format of various documents used in MOSE and the meaning of the parameters For more details see below 3 1 File Type The file types in MOSE are listed in Table 12 Table 12 Description of the file type in MOSE The file of the absorption results under TD The file of the transmittance results under TD The file of the absorption results under FD The file of the transmittance results under FD The file of the detection results under CW 3 2 Parameter File This section will specify the format of the parameter file in detail 3 2 1 Format of the Parameter File Table 13 Format specification of the parameter file 1 File type Format ASCII 2 0 O ASCII encoding version 2 0 corresponding to MOSE v2 1 2 comment This file is Comment generated by MOSE 2 SimulationProperty The keywords to start the setting of the simulation property Io m The forward simulation type BLT DOT or FMT The simulation dimension 2D or 3D a a LisourceNon o Ther namer othe tignsowres rsen fo meroa namper orhe tisesinmeions DetectorLensNum The total number of the detectors NOTE Need to set just in 3D CW MediumAlgorithm VRMC The algorithm of light propagation in medium FreeSpaceAlgorithm PINHOLE The algorithm of light propagation in free space NOTE Need to set just in 3D CW RO ae ee Region of Inte
31. he result as shown in Figures 58 59 High Threshold Low Threshold 0 Figure 58 Upper and lower threshold setting dialog box File Mesh Simplification Segmentation View Window Help 23 00000GE ii _ Ready HUM Figure 59 Display of threshold extraction result Select Output Segmentation Result output the result of threshold extraction in PLY OFF format to the project folder 2 4 2 Mesh Simplification The function is to simplify the object surface constructed by triangle meshes and thus reduce the data size However it also reduces the detailed description of the object surface Select File Load Data PLY OFF file and input PLY OFF format file the result is shown in Figure 60 Hose mewpro2 Image Processing gt File Mesh Simplification Segmentation View Window Help ria000008 amp Figure 60 Display of a mesh format file Select Mesh Simplification QEM Arithmetic and enter the dialog box Figure 61 of mesh simplification Set the target number of the mesh simplification the result is shown in Figures 62 Set Face Number Current Num Taget Num Figure 61 Dialog box of setting simplification Hose newpro4 Image Processing File Mesh Simplification Segmentation View Window Help lt Figure 62 Result of mesh simplification Select File Save Data Mesh Simplification Result save the simplified result to the project
32. le LightSourceProperty Internal The optical properties of the light source including four i Solid respects More information is listed in Table 14 NoSpecular 1 Internal External Set the position of the light source position Internal means inside of the medium and External means outside Solid Face Set the position of the photon Solid means the photon is generated inside the shape or on the boundary of the shape of the light source Face means the photon is generated just on the boundary of the shape Specular NoSpecular Specular means the specular reflectance will happen while the light source is outside the medium NoSpecular means no specular reflectance Exicitation Emission Exicitation means the light source is the incident laser Emission means it is the fluorophore NOTE Need to set just in FMT LightSourceCenter The center of the shape NOTE Need not to set while the shape is triangle mesh LightSourceAxis Half of the axis length of the shape NOTE Need not to set while the shape is triangle mesh see Figures 63 64 for more information LightSourcePath The path of the triangle mesh file used to describe the irregular shape NOTE Need to set while the shape is triangle mesh LightSourceSpectrumInde The optical properties of the light source Ke ee 1 Non Fluorophore the order is spectrum numb
33. le oe Table 24 Format of the absorption results in 2D Cartesian coordinate system under CW 2DCWAbsorption The total absorption in 2D at current spectrum CountX CountY The numbers of data along X axis and Y axis respectively 2DCWAbsorptionX Y The absorption results 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 Table 25 Format of the absorption results in 2D Polar coordinate system under CW 2DCWAbsorption The total absorption in 2D at current spectrum CountR CountA The numbers of data along radial direction and azimuth angle 2DCWAbsorptionRA The absorption results 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3 3 1 3 Detection Results The format of the detection results is shown in Table 22 Table 26 Format of the detection results under CW 3DTotalDetection The number of the detector and the total detection at current spectrum HeightResolution WidthResolution The numbers of data along the directions of height and width respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3 3 2 TD 3 3 2 1 Transmittance Results Compared to the transmittance results under CW the transmittance results under TD just increase the time as shown in Table 27 Table 27 Format of the transmittance results for the shape of triangle m
34. lts The format of the transmittance results is recorded according to the shape of the outermost tissue The format is shown in Table 15 while the shape is triangle mesh and the formats corresponding to other shapes are listed in Tables 16 21 Table 15 Format of the transmittance results for the shape of triangle mesh under CW Spectrum The central wavelength of the spectrum EE eee CountMeshFace The number of data which is equal to the number of mesh faces 3DCWTransmittanceMeshFace 0 00000e 000 One dimensional matrix data the order is the same as that of mesh faces in the shape file of triangle mesh CountMeshVertex The number of data which is equal to the number of mesh vertices 0 00000e 000 One dimensional matrix data the order is the same as that of mesh vertices in the shape file of triangle mesh NOTE The formats of the contents in the green part of the table above are same for all shapes and those in the blue part are different for different shapes The asterisk indicates the value Table 16 Format of the transmittance results for the shape of rectangle under CW 0 00000e 000 One dimensional matrix data 2DCWTransmittanceDown The total transmittance on the downside of the rectangle 2DCW TransmittanceDownX The transmittance results on the downside 0 00000e 000 One dimensional matrix data 2DCWTransmittanceLeft The total transmittance on the left side of the rectangle 2DCW TransmittanceLeftY The
35. m Spectrum Energy Excitation Wav Quantum Yield Figure 31 Dialog box of adding light source with irregular shape 4 Detector Interface As shown in Figure 33 the parameters of detector and lens can be set in this sub page The parameters in the list are described in detail below 3D Parameter Setting Medium Light Source Detector Simulation Property Load File Detector Index Vertical Plane FocalLength Add Spectrum Del Spectrum Spectrum Figure 33 Interface of setting the detector parameters Table 8 Description of the detector parameters Vertical Plane The plane of the detector perpendicular to Three options XY YZ ZX The central coordinate of the tissue shape along X axis The central coordinate of the tissue shape along Y axis The central coordinate of the tissue shape along Z axis Normal X The normal vector of the detector plane along X axis NOTE All normal vectors must point to the medium for imaging The normal vector of the detector plane along Y axis The normal vector of the detector plane along Z axis The image distance of the detector Click Add Detector users will enter the Add Detector dialog box Click Del Detector the optical parameters of the detector selected in the list will be deleted Add Detector Detector Parameter Yertical Plane XY Plane Focal Length ss Image Distance Lens Radius Center Poi
36. minY 4 416250 Bound maxY 57 676998 Bound minz 3 830420 Bound maxz 91 900101 Qhedim Qi eht Ready Figure 38 Interface of stopping the simulation running 2 2 2 4 Output Simulation Results Users can choose to output or show the simulation results after the end of the simulation successfully Output Simulation Parameter Output the simulation parameters to the project folder where the simulation is built on automatically Output 3D Simulation Result Output the simulation results including the absorption results the transmittance results and the detection results to the project folder Output CW TD FD Transmit Map To show the photon transmittance figures under CW TD and FD respectively Users can select the spectrum in the drop down box as shown in Figure 39 Hose newprol 3D Photon Transmittance Map r9 File Input Qutput Simulation View Window Help GB G GoeHee ee Output Graph CW Transmittance Map Select Spectrum 620 v skin heart liver lungs stomach Parameter Data path DAbj_ply bj_atl Face number Yertex number 25001 Bound minX 13 131900 Bound maxX 28 546499 Bound minY 4 416250 Bound maxY 57 676998 Bound minZ 3 830420 Bound maxZ 91 900101 Medium Qriat rete Osima Ready Figure 39 Photon transmittance figure Output CW Detector Map To show the photon detection figure under CW users can select the spectrum in the drop down box Salen mesm Ee and select the
37. nd Color Color Bar skin heart liver lungs stomach Projection Based on mesh Viewing Options Parameter Data path DAbj_ply bj_attl Face number 50000 i Mediun Li ght Figure 6 Point based Rendering Hose newprol 3D Photon Transmittance Map a rile Input Output Simulation Peery Window Help MG Vel ES v Status Bar Output Graph CW Transmittanc Select Plane Background Color Color Bar Based on vertex skin heart liver lungs stomach Projection v Based on mesh Viewing Options Parameter Data path DAbj_ply bj_attl Face number 50000 w Q Mediun GLi ght Figure 7 Surface based Rendering Projection Set the projection method in 3D including perspective projection and orthographic projection The effects are displayed in Figures 8 and 9 respectively Hose newpro1 3D Photon Transmittance rs File Input Output Simulation BAET Window Help op fe Zz of J Toolbar j pu o J v Status Bar Output Graph CW Transmittance Ftans Background Color Color Bar l Render Method heart Orthographic Projection liver Viewing Options lungs stomach Parameter Data path D bj_phybj_attl Face number 50000 i G edium Li zht Figure 8 Perspective Projection 2 Hose newprol 3D Photon Transmittance Map rts File Input Qutput Simulation Pe Window Help oP fe P lef i Toolbar l J ia a v Status Bar
38. nd source parameters corresponding to the new spectrum Add Spectrum Wavelength Io nm Tissue Optical Parameter Tissue Name Absorption 1 mm Scattering 1 mm Anisotropy Refractive Index PhantomSur face Light Source Optical Parameter X Humber of Photons Spectrum Energy Excitation Wav Quantum Yield At Figure 23 Dialog box of adding a new spectrum Click Del Spectrum uses can delete the selected spectrum shown as Fig 24 Click OR all the optical parameters of the tissues and the source parameters corresponding to the spectrum will be deleted DelSpectrum Choose Spectrum Cancel Figure 24 Dialog box of deleting a spectrum Click Apply users will save all the parameters on the interface Click Cancel users will quit the Parameter Setting dialog box without saving the parameters Click OK users will save all the parameters and quit the Parameter Setting dialog box 2 Medium Interface In MOSE the simulation object is defined as medium and it consists of homogeneous medium contains only one tissue and inhomogeneous medium contains more than one tissue Parameters used to define the tissue consist of the shape and the optical parameters The shape can be regular 2D Rectangle Ellipse 3D Cube Ellipsoid Cylinder or irregular Triangle mesh The optical parameters of the tissue consist of absorption coefficient scattering coefficient
39. ne x y plane yx plane xz plane z x plane y r plane z y plane Set the coordinate system of the view including XOY YOX XOZ ZOX YOZ ZOY Background Color Set the background color in view area There are three colors for choose including black white gray Color Bar There are five options for choose as shown in Figure 5 including Jet Autumn Spring Hot and Cool 2 Hose newprol 3D Photon Transmittance Map File Input Qutput Simulation BAE Window Help oP fe z of epee wo amp gt OAG LB D SY Status Bar Select Plane gt 620 v Background Color gt Bokmal STe Render Method b Autumn skin Projection b Spring heart a liver Viewing Options Cool lungs stomach Output Graph CW Transmittanc Parameter Data path D bj_ ply bj_att Face number 50000 i heiim QLight Figure 5 Set the color bar Render Method Render solution ow Based on vertex Based on mesh Render method includes point based and face based Point based adopt interpolation processing In the surface based each face has a single color Figure 6 and 7 shows the effect of the two kinds of render method Hose newprol 3D Photon Transmittance gt File Input Output Simulation DATA Window Help oP fe gt d El Toolbar Fig j 2 had i P v Status Bar Select Plane Output Graph CW Transmittanc Backgrou
40. nt mm Normal Yector A ze Detector Size mm Resolution Width 13 8 Width 12800 Cancel Figure 34 Dialog box of adding detector 5 Interface of Simulation Property In this sub page users can set the simulation properties of the light propagation in medium and free space as shown in Table 9 3D Parameter Setting Medium Light Source Detector Simulation Property Type of Forward Simulation Domain BLT O FMT DOT cw Absorption Cartesian Photon Density O Photon Fluence Transmittance Cartesian Separation O Minimum Maximum X axis mm 1 Y axis mm Z axis mm Radius mm Azimuth Angle Deflection Angle Time ps Frequency MHZ Thread Number Figure 35 Interface of setting the simulation properties Table 9 Description of the simulation properties l l The type of the forward simulation Including BLT DOT and Type of Forward Simulation FMT Users can choose any one at each simulation Simulation domain including CW TD and FD Users can choose Domain all at each simulation The simulation algorithm of light propagation in medium Medium Algorithm Type Currently the algorithms only have variance reduction Monte Carlo VRMC The simulation algorithm of light propagation in free space Free space Algorithm Type l l l S Currently the algorithm is based on pinhole projection Setting of the coordinate system
41. oading absorption data TT CTTTTTITITITITITITITITITITILIL LL Figure 3 Open a project 2 2 Optical Molecular Imaging 2 2 1 Introduction of the Interface The window interface of the optical molecular imaging project is shown in Figure 4 Menu Bar gt Hose newprol 3D Parameter Map file Input heart liver lungs stomach Side Bar Parameter Data Status Bar Figure 4 Main interface of MOSE The interface mainly includes five parts menu function button sidebar view area status bar Menu bar Menu bar includes all basic operations of MOSE mainly includes project operation new open close parameter input result output simulation control start and stop graphic display control operation of display window and so on Tool bar Some commonly used commands are arranged on the toolbar Side bar All the input parameters are shown on the side bar View area Display all the parameters and results Status bar Show the progress while writing or reading the simulation results 2 2 1 1 Menu Bar The upper part of main interface ranks a list of menus Each menu has different functions The followings are the detailed description of each function menu item Project Hew CtrltH Open Ctrlto Exit New Create a new project Open Open an existing project Close Close the current project Exit Exit MOSE Input SD Parameter 3D Parameter Input the simulation parameters in 3D
42. oblem is to reconstruct the optical properties of the inner tissues or the light sources There are three distinct technology domains for optical tomography that is the continuous wave CW the time domain TD and the frequency domain FD Each has distinct advantages and disadvantages and the selection of the appropriate technology depends on the specific application In order to realize high fidelity small animal imaging the non contact imaging approaches in free space is introduced recently compared to the traditional method using light guiding fibers Although the non contact imaging has become the mainstream it needs to consider the procedure of light propagation in free space and makes the research of light propagation in medium more difficult Molecular Optical Simulation Environment MOSE is a simulation platform for optical molecular imaging research co developed by Xidian University Institute of Automation Chinese Academy of Sciences China and Virginia Tech Wake Forest University School of Biomedical Engineering amp Sciences USA MOSE is featured by that it implements the simulation of near infrared light propagation both in medium with complicated shapes such as mouse and in free space Until now MOSE has realized the simulation of light propagation both in medium and in free space under CW TD and FD so it is a powerful tool to solve the forward problems in DOT FMT and BLT This manual will help users to learn how to use M
43. on Map Setting Phase Amplitude Phase Setting Setting Single layer Multilayer Single layer Select Spectrum 620 Select Spectrum 620 vi Plane Setting Plane Setting O x Y Plane CO xY Plane Total number 0 C Parallel to Z Axis C Parallel to Z Axis Total number 0 Separate the numbers with space a Single layer display setting b Multilayer display setting Figure 47 Settings of the absorption figure under FD with Cylindrical coordinate system Table 10 Description of the dialog boxes for displaying the absorption figure Select Spectrum Select the absorption results according to the spectrum Single layer Single layer display of the absorption results Multilayer display of the absorption results The numbers of the Multilayer layers are input by the dialog and separated by the space Select the number of time Select the number of the time under TD Amplitude Display the amplitude of the absorption results under FD 2 2 2 5 Open Project Users can also open the project built previously select Project Open in the menu bar or click the shortcut on the toolbar find out the previously saved project file MPJ and open it And then MOSE will load the related data corresponding to the project including the parameter file the absorption results the transmittance results and the detection results Fale Tnpot Qutpat Saaulation Vows Bondes falp tD bA in biie a Ouiput Graph Par
44. onding to Tables 2 and 4 Figure 28 shows the adding interface of the tissue with irregular shape corresponding to Tables 3 and 4 Add Tissue Tissue Parameter Name Is Outermost NO Shape Ellipsoid Center Position mm Half Axis mm o b 0 pe Optical Parameter Wavelengh fm Absorption 1 mm Scattering 1 mm Anisotropy Refr Figure 27 Dialog box of adding tissue with regular shape Add Tissue e Is Outermost Optical Parameter Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Re Figure 27 Dialog box of adding tissue with irregular shape 3 Light Source Interface The page of setting light parameter is the same as that of tissue in structure as shown in Figure 29 The first list displays the parameters corresponding to the light source with regular shape the second list displays the parameters corresponding to the light source with irregular shape the last list displays the optical parameters of the light source selected including the photon number the energy of the spectrum the excitation wavelength the quantum yield absorption factor and life time NOTE The last four parameters just belong to the fluorescence in the simulation of FMT 3D Parameter Setting Light Source Detector Simulation Property Light Source with Regular Shape z Shape X mm Y mm Z nm a nm b mm c nm Azimuthal Angle fh a a a spea Ellipsoid 15 000000 6
45. our types in the latest version of MOSE including BLT DOT FMT Excitation and FMT Emission The luminous type of the light source must be in accordance with the simulation type BLT DOT and FMT In FMT the luminous type of the light source can be set FMT Excitation or FMT Emission FMT Excitation means the light source is the incident laser and FMT Emission means the light source is the fluorophore which will be excited by the incident laser Table 6 Description of the parameters of the light source with irregular shape Shape File Path The path of the triangle mesh file used to describe the surface of the tissue The file format can be PLY OFF SURF MESH Change Path Change the path of triangle mesh file The rest parameters of the list are the same as that in Table 5 Table 7 Description of the optical parameters of the light source Wavelength The central wavelength of the spectrum Corresponding to the emission wavelength while the light source is fluorophore in FMT Number of Photons Number of the photons corresponding to the spectrum No need to set this parameter while the light source is fluorophore in FMT Spectrum Energy The energy of the light source corresponding to the spectrum No need to set this parameter while the light source is fluorophore in FMT Excitation Wavelength nm The excitation wavelength of the fluorophore in Quantum Yield The quantum yield of the fluoresc
46. pdate accordingly 3 Why the process of MOSE still reside in the task manager after close the program Because some memory has not been released after close MOSE it maybe still resides in the task manager The process needs to be closed by user manually in task manager MOSE is developed for research institute it is not perfect and we will continuously improve it
47. rest ROI Unit mm please refer to Figure 65 1 3D The order is Xmin Xmax Ymin Ymax Zmin Zmax Rmin Rmax Amin Amax Dmin Dmax which are corresponding to the minimums and the maximums along the directions of X axis Y axis Z axis radial azimuth angle and deflection angle respectively 2 2D The order is Xmin Xmax Ymin Ymax Rmin Rmax Amin Amax which are corresponding to the minimums and the maximums along the directions of X axis Y axis radial and azimuth angle respectively ROJISeparation The separations of ROI Unit mm please refer to Figure 65 1 3D The order is Dx Dy Dz Dr Da Dd which are corresponding to the format of ROI in 3D 2 2D The order is Dx Dy Dr Da which are corresponding to the format of ROI in 2D AbsorptionMatrix Cartesian The coordinate system for saving the absorption results 1 3D Cartesian Cylindrical 2 2D Cartesian Polar TransmittanceMatrix Cartesian The coordinate system for saving the transmittance results It s related to the shape of the outmost tissue The program will automatically modify the wrong setting of the coordinate system NOTE For the Cylinder shape there are two choices of coordinate system including Cartesian and Cylindrical However there is only one choice for other shapes such as ellipse Polar rectangle Cartesian ellipsoid Spherical cube Cartesian
48. s of the 2D shapes Point O is the center a b are the half of the axis length along X axis and Y axis respectively Radial Direction Figure 65 Illustration of the ROI which need to set the minimum and the maximum along six directions including X axis Y axis Z axis radial azimuth angle and deflection angle The six directions are shown in figure 3 2 3 Structure Design of the Detector Case 1 Diagram of the detector perpendicular to X Y Plane in 3D Case Top View Pa i H A N La M al Y iy 7 i a Width X Width x Figure 66 View of the detector perpendicular to X Y plane the normal vector of the detector is 0 Case 2 Diagram of the detector perpendicular to X Z Plane 7 7 in 3D Case 2 Side ad Width Figure 67 View of the detector perpendicular to X Z plane the normal vector of the detector is 0 Case 3 Diagram of the detector perpendicular to Y Z Plane z in 3D Case 3 F Width Figure 66 View of the detector perpendicular to Y Z plane the normal vector of the detector is 0 3 3 Format of the Simulation Results There are three simulation domains in MOSE including CW TD and FD The description of the simulation results are also divided into three parts correspondingly The simulation results include the transmittance results the absorption results and the detection results 3 3 1 CW 3 3 1 1 Transmittance Resu
49. scribe the tissue boundary constructed by triangle mesh 9 Improve the stability of the software and the efficiency of the simulation algorithms 1 3 Install and Uninstall System requirements MOSE is now complied under Windows so it can only be run on Windows 2000 XP Vista 7 Install Download the latest version of MOSE from http www mosetm net MOSE is green software no installation and can be used directly after the decompression User need to choose the right version 32 Bit or 64 Bit according to the version 32 Bit or 64 Bit of Windows Uninstall Since MOSE is green software you can uninstall it after deleting the folder of MOSE directly 2 Detailed Specification This chapter will conduct a more detailed description of use including four sections project optical molecular imaging 2D 3D energy mapping and image processing 2 1 Project In MOSE all functions are managed independently by the project At present MOSE contains three project types optical molecular imaging 2D 3D energy mapping and image processing These three project types have different functions respectively As follows 1 Optical Molecular Imaging Contains three types of forward simulation of optical molecular imaging Such as BLT FMT and DOT 2 2D 3D Energy Mapping Contains the function of mapping the fluence detected by 2D CCD to the flux on the 3D surface of the medium 3 Image Processing Contains threshold extraction of CT raw data
50. transmittance results on the left side 0 00000e 000 One dimensional matrix data 2DCWTransmittanceRight The total transmittance on the right side of the rectangle 2DCWTransmittanceRightY The transmittance results on the right side 0 00000e 000 One dimensional matrix data Table 17 Format of the transmittance results for the shape of ellipse under CW 0 00000e 000 One dimensional matrix data Table 18 Format of the transmittance results for the shape of ellipsoid under CW CountD CountA The numbers of data along the directions of deflection angle and azimuth angle respectively 00000e 000 0 00000e 000 Two dimensional matrix data the order is 0 0 0 1 0 CountA 1 O 1 1 1 CountA CountD 0 CountD CountA Table 19 Format of the transmittance results for the shape of cylinder in Cylindrical coordinate system under CW 3DCWTransmittanceSide AZ CountA CountZ The numbers of data along azimuth angle direction and Z axis respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in oe Table 18 CountR CountA The numbers of data along radial direction and azimuth angle direction respectively 3DCWTransmittanceTopRA The transmittance results on the top 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceBottom The total transmittance on the bottom of the cylinder
51. ttanceFronty Z The transmittance results on the front side 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3DCWTransmittanceBack The total transmittance on the top side of the cube CountY CountZ The numbers of data along Y axis and Z axis respectively 3DCW TransmittanceBack YZ The transmittance results on the back side 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 18 3 3 1 2 Absorption results The format of the absorption results is recorded according to the coordinate system The format in Cartesian coordinate system is shown in Table 22 and the formats in other coordinate systems are listed in Tables 23 25 Table 22 Format of the absorption results in 3D Cartesian coordinate system under CW The numbers of data along X axis Y axis and Z axis respectively 0 00000e 000 0 00000e 000 Three dimensional matrix data the order is 0 0 0 0 0 1 0 0 CountZ 0 1 0 0 1 1 0 1 CountZ 0 CountY 0 0 CountY 1 0 CountY CountZ CountX CountY 0 CountX CountY 1 CountX CountY CountZ Table 23 Format of the absorption results in 3D Cylindrical coordinate system under CW CountR CountA CountZ The numbers of data along radial direction azimuth angle direction and Z axis respectively 0 00000e 000 0 00000e 000 Three dimensional matrix data the order is the same as that in Tab
52. ulation may fail The shape of the tissue maybe regular 2D Rectangle Ellipse 3D Cube Ellipsoid Cylinder or irregular Triangle The central coordinate of the tissue shape along X axis NOTE All units of the length in MOSE are millimeter Half of the axis length of the tissue shape along X axis NOTE the half of the axis length has different meanings to different shape please refer to Figures 63 64 in Section 399 Half of the axis length of the tissue shape along Y axis c mm Half of the axis length of the tissue shape along Z axis Table 3 Description of the parameters of the tissue with irregular shape The name of the tissue The number of the tissue in the tissue list of the medium Outermost Outermost flag Shape File Path The path of the triangle mesh file used to describe the surface of the tissue The file format can be PLY OFF SURF MESH Table 4 Description of the optical parameters of the tissue Click Add Tissue the selection dialog box Shape Type pops up as shown in Figure 26 Click Del Tissue the shape parameters and optical parameters of the tissue selected in the list will be deleted Shape Type Triangle Meshj off ply surf mesh Figure 26 Selection dialog box of the tissue shape After selecting the type of the shape users will enter the interface shown in Figure 27 or 28 Fig 27 shows the adding interface of the tissue with regular shape corresp

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