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1. a The boundary of the mouse surface Hose newProject Image Processing lt P File Mesh Simplification Segmentation Mesh Extraction View Window Help LiL i E b The boundary of the liver Figure 63 Extraction results of the digimouse 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 14 Table 14 Description of the file type in MOSE File extensions File description File content Project file for MOSE Save the information in a MOSE 45 The file of the simulation Save the optical simulation parameters in parameters an MC simulation The file of the absorption results Save the absorption results under CW in under CW an MC simulation The file of the transmission Save the transmittance results under CW results under CW in an MC simulation The file of the fiber detector Save the detector results under CW in an results under CW MC simulation The file of the absorption results Save the absorption results under TD in an under TD MC simulation The file of the transmittance Save the transmittance results under TD in results under TD an MC simulation The file of the absorption results Save the absorption results under FD in an under FD MC simulation The file of the transmittance Save the
2. CI X Z Plane a Single layer display setting b Multilayer display setting Figure 39 Settings for the absorption figure under CW using a Cartesian coordinate system Time Domain Absorption Map Setting Time Domain Absorption Map Setting Select the number of time Select the number of time J Single layer Multilayer O Single layer Setting Setting Select Spectrum 620 Select Spectrum Plane Setting Plane Setting CI x Y Plane CI x Y Plane Total number 0 a O Y Z Plane CO YZ Plane Total number 0 OXZ Plane OxzZ Plane Total number 0 Seperate the numbers with space a Single layer display setting b Multilayer display setting Figure 40 Settings for the absorption figure under TD using a Cartesian coordinate system 32 Frequency Domain Absorption Hap Setting Phase Setting Single layer Multilayer Select Spectrum 620 Plane Setting L XY Plane CO Y Z Plane CO X Z Plane a Single layer display setting Figure 41 Settings for the absorption figure under FD using a Cartesian coordinate system amp Hose newProject 3D Photon Absorption Map ris WwW LJ O Absorption Map Setting A Output Graph CW Multilayer Single layer Setting Select Spectrum 620 Plane Setting XY Plane Y Z Plane 112174 Figure 42 Absorption figure using a single layer display under CW with a Cartesian coordina
3. DOT or FMT The simulation dimension 2D or 3D LightSourceNum oe The total number of light sources TissueNum JO The total number of the tissues in the medium DetectorLensNum The total number of detectors NOTE Need to set it in 3D CW MediumAlgorithm VRMC The algorithm of light propagation in the medium FreeSpaceAlgorithm ROISeparation AbsorptionMatrix TransmittanceMatrix PINHOLE Cartesian The algorithm of light propagation in free space NOTE Need to set it in 3D CW Region of Interest ROD Unit mm please refer to Figure 65 1 3D The order is Xmin Xmax Ymin Ymax Zmin Zmax Rmin Rmax Amin Amax Dmin and Dmax which corresponds to the minimum and maximum values along the directions of the 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 and Amax which correspond to the minimum and the maximum values along the directions of the X axis Y axis radial and azimuth angle respectively The separations of the ROI Unit mm please refer to Figure 65 1 3D The order is Dx Dy Dz Dr Da and Dd which correspond to the format of the ROI in 3D 2 2D The order is Dx Dy Dr and Da which correspond to the format of the ROI in 2D The coordinate system for saving the absorption results 1 3D Cartesian Cylindrica
4. G Figure 27 Dialog box of the added light source with a regular shape Add Light Source Light Source Parameter Photon Emitting Azimuthal Angle Deflect Angle Internal Solid Specular Property Wavelength nm lt m Figure 28 Dialog box of the added light source with an irregular shape 4 Detector Interface As shown in Figure 29 the parameters of the detector and lens can be set on this sub page The parameters on the list are described in detail below 24 3D Parameter Setting Medium Light Source Detector Simulation Property Detector Add Fiber Add CCD Figure 29 Interface of the setting of the detector parameters Table 8 Description of the CCD detector parameters Vertical Plane The plane of the detector that its perpendicular to three options XY YZ and ZX The central coordinate of the tissue shape along the X axis The central coordinate of the tissue shape along the Y axis The central coordinate of the tissue shape along the Z axis Normal X The normal vector of the detector plane along the X axis NOTE All normal vectors must point to the medium for imaging Click Add CCD and users will enter the Add Detector dialog box as shown in Figure 30 25 Add Detector Detector Parameter Vertical Plane Y Plane Focal Length Image Distance 2 5403 Lens Radius yo Center Point mm Normal Yector pd Z CN COS Yi 0 i
5. Spectrum Energy The energy of the light source corresponding to the spectrum no need to set this parameter while the light source is a fluorophore in FMT Excitation Wavelength nm The excitation wavelength of the fluorophore in FMT Quantum Yield The quantum yield of the fluorescence in FMT Absorption Factor The absorption factor of the fluorescence in FMT Life Time The life time of the fluorescence in FMT Unit ps Click Add Light Source and the selection dialog box Shape Type will pop up as shown in Figure 26 Click Del Light Source and the optical parameters of the light source selected in the list will be deleted Shape Type Triangle Mesh off ply surf Figure 26 Selection dialog box of the light source shape After selecting the shape users will enter the interface shown in Figure 27 or 28 Figure 27 shows the added interface of the light source with a regular shape corresponding to Tables 5 and 7 Figure 28 shows the added interface of the light source with an irregular shape corresponding to Tables 6 and 7 23 Add Light Source Light Source Parameter Shape ARTIGE v Luminous Type BLT Center Position mm Half Axis mm Internal vi o y Solid 539 MO 3 Specular Photon Emitting Azimuthal Angle Deflect Angle Min 0 degree Min a degree Max 360 degree Max degree Property Wavelength nm Number Of Photons Spectrum Energy Excitation Wav
6. The keywords to end the setting of the simulation property 3 Spectrum Spectrum list where the order is the spectrum number and the central wavelength of the spectrum Unit nanometer For example Spectrum 1 650 Spectrum 2 690 4 LightSource The light source parameters and their numbers LightSourceShape The shape of the light source 1 3D Ellipsoid Cylinder Cube and TriangleMesh Irregular shape 2 2D Ellipse Rectangle LightSourceProperty Internal The optical properties of the light source including four of its Solid aspects More information is listed in Table 14 NoSpecular 1 Internal External Set the position of the light source position where Internal means inside of the medium and External means outside of it 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 occur while the light source is outside of 48 the medium NoSpecular means no specular reflectance Excitation Emission Excitation means the light source is the incident laser Emission means it is the fluorophore NOTE Need to set it in FMT LightSourceCenter The ce
7. Figure 44 Settings for the absorption figure under TD using a Cylindrical coordinate system Frequency Domain Absorption Map Setting x Frequency Domain Absorption Map Setting Phase Amplitude Phase Setting Setting Single layer Multilayer Single layer Select Spectrum 620 Select Spectrum 620 Y Plane Setting Plane Setting LIX Y Plane LIX Y Plane Total number 0 C Parallel to Z Axis C Parallel to Z Axis Total number 0 x Z Plane X 7 Plane otal number Separate the numbers with space a Single layer display setting b Multilayer display setting 34 Figure 45 Settings for the absorption figure under FD using a Cylindrical coordinate system Table 11 Description of the dialog boxes for displaying the absorption figure Single layer Single layer display of the absorption results Multilayer display of the absorption results The numbers of the Multilayer layers are inputted by the dialog and separated with a 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 by selecting Project Open from the menu bar or by clicking the shortcut on the toolbar to find the previously saved project file MPJ and open 1t MOSE will then load the related data corresponding to the project including the param
8. the order of each line is x y and z coordinates of each vertex 2 Triangle mesh data The first part is the number of triangle meshes In the second part the order of each line is the vertex indices of each triangle mesh The index starts from 1 AM Instruction The tetrahedral mesh file is generated from Amira so for more information please refer to http www amira com MESH Instruction The tetrahedral mesh file is generated from Netgen http www hpfem jku at netgen which consists of three parts 1 Vertex data The first part 1s the number of vertices In the second part the order of each line is x y and z coordinates of each vertex 65 2 Tetrahedral data The first part is the number of tetrahedrons In the second part the order of each line is the region index of each tetrahedron it belongs to as well as the vertex indices of each tetrahedron Both indices of the region and the vertex begin at 1 3 Boundary triangle mesh from different regions Note This part is not used by MOSE thus 1t should be omitted The first part is the number of triangle meshes In the second part the order of each line is the region index of each triangle mesh it belongs to as well as the vertex indices of each triangle mesh Both indices of the region and the vertex start from 1 STL Instruction Only the triangle mesh file in a PLY format 1s supported by MOSE for example solid name facet normal ni nj nk outer loop v
9. 20 3 3 1 2 Absorption results The format of the absorption results is recorded based on the coordinate system The format in the Cartesian coordinate system is shown in Table 25 and the formats in the other coordinate systems are listed in Tables 25 28 Table 25 Format of the absorption results in a 3D Cartesian coordinate system under CW 60 The central wavelength of the spectrum Domain CW The simulation domain 3DCWAbsorption The total absorption in 3D at the current spectrum CountX CountY CountZ The numbers of data along the X axis Y axis and Z axis respectively 3DCWAbsorptionX YZ The absorption results 0 00000e 000 0 00000e 000 Three dimensional matrix data where the order is 0 0 0 00 1 00 CountZ O0 1 O 0 1 1 0 1 CountZ O CountY 0 0 CountY 1 0 CountY CountZ CountX CountY 0 CountX CountY 1 CountX CountY CountZ Table 26 Format of the absorption results in a 3D Cylindrical coordinate system under CW CountR CountA CountZ The numbers of data along the 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 Table 24 Table 27 Format of the absorption results in a 2D Cartesian coordinate system under CW 2DCWAbsorption The total absorption in 2D at the current spectrum CountX CountY The numbers of data along the X axis and Y axis respective
10. 42 2 4 3 Tetrahedral Boundary Extraction vi A E ia aiees 43 3 Description of the File Format in MOSE ooooocccnnnnnnnncncncnnnonnnonoonnnnnnnnnnnnnnnnonnnnnnonnnonnnnnnnnnnnnnnnnnnnnnnss 45 S D O o E EE A E E EAE E PU O E E E E E A S 45 32 Parameter File rroe EE EE E E N E TA 46 IAk Fornar orhe Paraneter File st dali bii cid 46 3 2 2 Description of the Light Source Medium Model Detector and Region of Interest EE E A E O E T 50 D2 2 NON 50 9522 NIC CUM Md estas Grn ee Ge Gee ee Gee Glee 51 22 PLE DEE E 53 e O III deh ctedsudiateltedahard 55 A A NR A A E 55 33 Format of the Simulation Results irirna a A eee es 56 dl SETS 57 Ili Transmittance Results aras a R a a 57 IZ A DSO LON TESU ING ai E 60 Deal Plane Detector CS UG stasis es rhein OS 61 Jo Lo PIBER Detector Results sona lit iii di ae 62 NO AA o e S PEPE A E E 62 II FILA DSOMOO lA O TO Son A O leads 63 O A A A A AA 64 a i Transmittance Resulta ala lola lada lado dea bd 64 3 353 2 A DSOFPLION REUS eS 64 O a AE A A ta OE EEE A EEE EE bats ee aes 65 4 Frequently Asked Questions FAQ riesila n a aN 66 MI 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 biomedica
11. fib Project Path H MOSE tesi Select Project Type Optical Molecular Imaging Forward Simulation of BLT DOT or FMT Simulation Dimension O 2D O 3D O 2D 3D Energy Mapping O Image Processing Surface Reconstruction Surface Simplification Tetrahedron Boundary Extraction Figure 2 Build a new project iGo Seuecogn Output Graph Select Spectrum Part 1 2 Optical simulation in medium 31 6 Execute Time O d 00 h 00 m 20 s A ave i 7 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 Status Bar Figure 4 Main interface of MOSE The interface mainly includes five parts menu function button view area and status bar Menu bar Menu bar includes all of the basic operations of MOSE but it 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 View area Display all of 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 the main interface ranks a list of menus Each menu has different functions The following section 1s the detailed description of e
12. is generated on the boundary of the shape Specular Flag YES means the specular reflectance will happen while the light source is outside of the medium NO means no specular reflectance Luminous Type Luminous type of the light source There are four types in the 22 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 as FMT Excitation or FMT Emission where 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 an 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 the triangle mesh file The rest parameters on 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 corresponds to the emission wavelength while the light source is a fluorophore in FMT Number of Photons Number of photons corresponding to the spectrum no need to set this parameter while the light source is a fluorophore in FMT
13. min 0 00e 000 Figure 9 Orthographic projection Show Photon Trajectory Set whether or not to show the photon running path in the process of simulation After setting it the view will display the path of each photon running However this will largely reduce the simulation speed Do not suggest users to set this item The result is displayed in Figure 10 x Project Input Output Simulation View Window Help ox Output Graph Select Spectrum Part 1 2 Optical simulation in medium 1 0 Execute Time 0 d 00 h 00 m 28s Ready NUM Figure 10 Show photon trajectory Viewing Options Set display properties of the medium the light source and the detector in different types of maps parameter map absorption map and transmittance map including color opacity and show hide and solid wireframe as shown in Figures 11 and 12 11 Color Property in Parameter Hap Medium Light Source Detector 50 TES TES surface 50 TES TES stomach 50 TES TES TES TES TES TES TES TES o Caca Figure 11 Display properties setting A Bose newProject 30 Parameter Kap gt Project spat utpat isalatioa Vier Pinder Help GJO HS Lad Fo DIE Output Graph Parameli Select Spectrum Figure 12 Display properties rendering Window Window Help Cascade ij Tile Arrange Icons 12 Set the view s layout Cascade View cascade Tile View tile Arrange Icons Arrange Icons
14. parameters of a tissue with a regular shape The name of the tissue The number of the tissue on 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 simulation may fail Shape The shape of the tissue may be regular 2D rectangle ellipse 3D cube Ellipsoid cylinder or irregular triangle mesh X mm The central coordinate of the tissue shape along the X axis NOTE All units of length in MOSE are in millimeters The central coordinate of the tissue shape along the Y axis 19 The central coordinate of the tissue shape along the Z axis Half of the axis length of the tissue shape along the X axis NOTE half of the axis length has different meanings based on the different shape so please refer to Figures 63 and 64 in Section 3 2 2 Table 3 Description of the parameters of the tissue 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 Table 4 Description of the optical parameters of the tissue Anisotropy Anisotropy factor Refractive Index Refractive index Click Add Tissue and the selection dialog box Shape Type wil
15. w Requested 2621 44 bytes Filesize 0 bytes Width Pixel interval Height Pixel interval Number of slice alice interval Number of channels Little Endian Head length Interleaved Storing Figure 54 Dialog box for reading the RAW format file Table 13 Description of the parameter setting while reading the RAW format file Filename The path of the RAW IMG file Data type The data type of the RAW IMG file Requested Calculated size of the file according to the input parameters Check the accuracy 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 should look like that in Figure 55 if the input data are correct 40 File Mesh Simplification Segmentation Mesh Extraction View Window Help Ready Figure 55 Display after reading the RAW format file Select Segmentation Threshold Segmentation which provides a threshold setting dialog box Set the upper and lower threshold and obtain the results as shown in Figures 56 and 57 High Threshold Low Threshold 0 Figure 56 Upper and lower threshold settings in the dialog box File Mesh Simplification Segmentation Mesh
16. Data Type O Regular Shape Triangle Mesh Tetrahedron Medium File D mose_v2 2_32bit optical molecular imaging mouse_tetrahedron mesh Tissue with Regular Shape Tissue Wane Index Outernost Shape X aa Y Ga Z Gam a om b Goa lt om ssut _Tissue jular Shape Triangle Mesh Tetrahedron r Optical Parameter of surface erated Go iena 0 0 seis 0 0 pairere Rte aa em io os oo mo 10 000000 0 900000 P a Load the Independent medium model Medium Liqht Source Detector Simulation Property Medium Data Type Tissue with Regular Shape Tissue Nuno Index Outernost shape x an Y aa Z Gn Ga b om c Gnd Shape File Path Y D mose_v2 2_32bit optical molecular imaging mouse_surface off xl D mose_v2 2_32bit optical molecular imaging mouse_heart off gt D mose_v2 2_32bit optical molecular imaging mouse_stomach off zi D mose_v2 2_32bit optical molecular imaging mouse_lung off Optical Parameter of surface res Go arepa 0 0 setting 0 0 tier Rte Sader eo o ios o mo 10 000000 0 900000 b Load the Integral medium model Figure 18 Dialog box of loading the parameter file 17 2 2 2 2 2 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 the parameter set
17. Extraction View Window Help Ly bed Ly ha id ew LU E ES Ready Figure 57 Display of the threshold extraction result Select Output Segmentation Result the extraction result would be saved in PLY OFF 41 format in the project folder 2 4 2 Mesh Simplification The function is to simplify the object surface constructed by the 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 the PLY OFF format file The result is shown in Figure 56 Nose newProject 3D Nesh QEN Simplification Map Mesh Simplification Segmentation Mesh Extraction View Window Help je gt Pao Figure 58 Display of a mesh format file Select Mesh Simplification QEM Arithmetic and enter the dialog box Figure 59 of the mesh simplification Set the target number of the mesh simplification the result is shown in Figure 60 Set Face Humber Current Num Taget Num 3000 Figure 59 Dialog box for setting the simplification 42 Hose newProject Image Processing File Mesh Simplification Segmentation Mesh Extraction View Window Help LJ G K ha lus hd EJ E E Figure 60 Result of the mesh simplification Select File Save Data Mesh Simplification Result and save the simplified result to the project folder 2 4 3 Tetrahedral Boundary Extrac
18. Help About Mose Help Files About MOSE Display the version and copyright information for MOSE Help Files Show the help file for MOSE 2 2 1 2 Tool Bar The toolbar is a series of function button combinations which provides a shortcut method to perform common commands Table 1 Description of the toolbar Function Input parameters Save parameters results Reset coordinate axis Start simulation Stop simulation Show Hide colorbar Screenshot 13 2 2 1 3 View Area View area 1s the display area mainly responsible for displaying the simulation parameters and the simulation results as shown in Figure 13 Figure 13 View area Some operations of the view area have been introduced in the section of the menu bar In addition clicking the right middle and left mouse buttons can operate the rotation move and enlarge reduce operations respectively The simulation parameters map photon absorption map photon transmittance map and photon detection map can be selected from the output menu or output graph on the toolbar as shown in Figure 14 Output graph Parameter Mar C Absorption Map C CCD Map CAR Transmittance Mar Figure 14 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 the simulation results as shown in Figure 15 14 E x DOsSdacoua Output Graph Parameter Map Select Spect
19. 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 3 Last update 2011 3 21 Jie Tian Ph D tian ieee org Jimin Liang Ph D jimleung mail xidian edu cn Shenghan Ren Ph D Candidate renshenghan O gmail com Ge Wang Ph D wangge O vt edu Catalogue PAD OUT MOS Bi ias 1 A e eo II a l 12 New Feat reSiecnei a E asieuauragdacanudewasawanes canes E R A l IS JBeature Leto Version 2 oido 2 Fastland Umata nanea ida dd 3 2 Eta PE CHICA CON NA ATAN ARAS AAN N 3 ZA PNC iii 3 22 Optical Molecular dns a cd 5 2 2 1 Introduction of the Interface occccccccnnnononoonnnnonncnncnnnonnnnnnnonnnnonnnononnnnncnnnnnnnnnnnnnnnos 5 A AA A O terete Meta EE E ea nal T AT 6 X22 OLD A i EE 13 EA IS PA A O O O A TE rere errs ee 14 ATA ES E1 A MORTEM Or eT E Ronen amr A Den Mee per ni at Mer emer ETA 14 SIS POI E Ipe A A A A 15 A NOW PTO TEO 15 2 2 2 2 Input Simulation Parameters onden E A 16 2 2 2 3 Start SMU Oeae E EEE EEE EEEREN 29 2 2 2 4 Output simulation Result unit inn 30 2D 2D OEM PTOJOC enira 35 2 rEnerS yY Mippin From 2010 3D iii 36 ZA Made Procesado 39 2351 Cires hold EXT aconse a a a A A 39 24 2 Mesh Simp UMCA ON dis
20. WEiberDetectorTop CountX CountY 3DCWFiberDetectorTopX Y 0 00000e 000 0 00000e 000 3DCWFiberDetectorBottom 3DCWFiberDetectorBottomX Y 0 00000e 000 0 00000e 000 CountD CountA 3DCWTransmittanceSideDA 0 00000e 000 0 00000e 000 as that in Table 20 The detection of the detector on the top when the shape of the detector is cylinder The numbers of data along the X axis and Y axis respectively on the top Two dimensional matrix data the order is the same as that in Table 20 The detection of the detector on the bottom when the shape of the detector is cylinder Two dimensional matrix data the order is the same as that in Table 20 The numbers of data along the directions of the deflection angle and azimuth angle respectively Two dimensional matrix data the order is the same as that in Table 20 3 3 2 TD 3 3 2 1 Transmittance Results Compared to the transmittance results under CW the transmittance results under TD only increase the time as shown in Table 31 62 Table 31 Format of the transmittance results for the shape of a triangle mesh under TD Domain TD The simulation domain 3DTDTransmittanceMesh The total transmittance of the triangle meshes in the first time segment CountMeshFace Same as that in Table 17 3DTDTransmittanceMeshFace The transmittance results on each mesh face in the first time segment 0 00000e 000 Same as that in Table 17 CountMesh Vertex Sam
21. X axis the direction of the Y axis the direction of the Z axis the radial direction the azimuth direction and the direction of deflection angle respectively The ROI is determined by the starting and end points and it also has some connection with the coordinate system selected by the user P is a point in 3D of which the X Y Z the radial value the azimuth angle and the deflection angle are all shown in Figure 68 2 ROISeparation The unit intervals of all of the directions in the ROI NOTE While setting the ROI and ROISeparation in the parameter file the user must obey the order mentioned above and no value can be skipped The setting of the coordinate system for saving the absorption result and the transmittance result contains two of the following 1 AbsorptionMatrix Coordinate system for saving the absorption matrix there is the Cartesian coordinate system and Polar coordinate system in 2D and there is the Cartesian coordinate system and cylindrical coordinate system in 3D 2 TransmittanceMatrix Coordinate system for saving the transmittance matrix The set of the coordinate system is also restricted by the shape of the outermost boundary of the medium Rectangle Cartesian coordinate system ellipse Polar coordinate system cube Cartesian coordinate system ellipsoidal Spherical coordinate system and Cylinder Cartesian or Cylindrical coordinate systems which only affect the manner of saving the results on up
22. ach function menu item Project Me Ctrl H Open Ctr1 0 Close 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 into a 3D 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 where the document suffix is MSE 3D Simulation Result After completing the simulation output the simulation results to the constructed project folder including the 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 Simulation Start Start the simulation Stop Stop the simulation during the simulation process and the progra
23. ahedral mesh structure and are joined together as shown in Figure 65 this kind of media model is called the Integral medium model The differences between the medium models arise from the differences between the realizations of the MC simulation method but users only need to know how to set the correct structure for the medium without fully knowing the details of the program as described in the following a a Illustration of the parameters of the 2D shapes Point O is the center while a and b are the halves of the axis length along the X axis and Y axis respectively b Illustration of the parameters of the 3D shapes Point O is the center while a b and c are the halves of the axis length along the X axis Y axis and Z axis respectively 51 c Irregular triangle mesh structure with an empty interior this 1s the shape of a stomach Figure 64 Illustration of different shapes in an independent medium model Figure 63 Integral media model irregular tetrahedral mesh structure Only the boundaries of the regions are shown here The interior is constructed by tetrahedrons it is a whole structure of a mouse which consists of the heart lungs stomach liver and kidneys Tissue 1 rectangle set as the outermost tissue Integrate to an Tissues independent Tissue 2 ellipse medium model Tissue Tissue 3 rectangle Note The actual region of tissue 1 is the gray part Tissue 4 triangl
24. bsorption Results Compared to the absorption results under CW the absorption results under FD include amplitude and phase as shown in Table 34 Table 34 Format of the absorption results in a 3D Cartesian coordinate system under FD CountX CountY CountZ Same as that in Table 24 3DFDAmpAbsorptionX YZ The amplitude of the absorption in a 3D Cartesian coordinate system 0 00000e 000 0 00000e 000 Same as that in Table 24 64 3DFDPhaAbsorptionX YZ The phase of the absorption in a 3D Cartesian coordinate system 0 00000e 000 0 00000e 000 Same as that in Table 24 3 4 Other files In MOSE there are other types of files except for the optical simulation parameters and simulation results file RAW IMG IM0 DICOM Instruction Image data used in the image processing OFF Instruction Only the triangle mesh file in the OFF format is supported by MOSE 1 The numbers of vertices and triangle meshes 2 Vertex data The order of each line is x y and z coordinates for each vertex 3 Triangle mesh data The order of each line is the vertex number of each mesh triangle mesh 1s 3 and the vertex indices of each triangle mesh The index begins from 0 PLY Instruction Only the triangle mesh file in a PLY format is supported by MOSE for more information please refer to http paulbourke net dataformats ply SURF Instruction 1 Vertex data The first part is the number of vertices In the second part
25. ce for stopping the simulation run 2 2 2 4 Output Simulation Results Users can choose to output or show the simulation results successfully at the end of the simulation Output Simulation Parameter Output of the simulation parameters in the project folder Output 3D Simulation Result Output of the simulation results placed in the project folder including the absorption results the transmittance results and the detection results Output CW TD FD Transmit Map To show the photon transmittance figures under CW TD and FD respectively Users can select the spectrum from the drop down box as shown in Figure 36 Hose newProject 3D Photon Transmittance Kap gt Project Input Output Simulation View Window Help LJ Ly 3 Ly las oO Wi Output Graph CW Transmittance Map Select Spectrum 620 v Figure 36 Photon transmittance figure Output CW CCD Detector Map To show the photon detection figure under CW users can select the spectrum from the drop down box E and select the detector number from the drop down box PetectorNum 1 Y and the order of the numbers will be in accordance with the order of the detectors in the parameter file as shown in Figure 37 30 gt Project Input Output Simulation View Window Help Output Graph CW Detector Map Select Spectrum 620 Detector Num 1 max 8 72e 005 min 0 00e 000 Ready HUM Figure 37 Plane detector figure Output CW Fiber Detector Map To show the phot
26. ce results for the shape of an ellipsoid under CW 3DCWTransmittanceSide The total transmittance on the side of the ellipsoid 58 CountD CountA The numbers of data along the directions of the deflection angle and azimuth angle respectively 3DCWTransmittanceSideDA The transmittance results on the side 0 00000e 000 0 00000e 000 Two dimensional matrix data where the order is 00 0 1 0 CountA 10 1 1 1 CountA CountD 0 CountD CountA Table 22 Format of the transmittance results for the shape of a cylinder in the Cylindrical coordinate system under CW 3DCWTransmittanceSideAZ CountA CountZ The numbers of data along the azimuth angle direction and Z axis respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order 1s the same as that in Table 20 3DCWTransmittanceTop The total transmittance on the top of the cylinder CountR CountA The numbers of data along the radial direction and azimuth angle direction respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in eN Table 20 3DCWTransmittanceBottom CountR CountA The numbers of data along the radial direction and azimuth angle direction respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 20 Table 23 Format of the transmittance results for the shape of a cylinder in the Cartesian coordinate syst
27. ct Name newProject Project Path ss Select Project Type Optical Molecular Imaging Forward Simulation of BLT DOT or FMT Simulation Dimension geseeseseeseesoussoccccceseseesosossssssoseoesessssssoosossssssssosessssssss Image Processing Surface Reconstruction Surface Simplification Tetrahedron Boundary Extraction MI Ready Figure 47 Building a project for 2D 3D energy mapping The interface is shown in Figure 48 after clicking OK amp Mose newProject2D 3D Energy Mapping Project Input Output Mapping View Window Help JO Ds CY Output Graph Select Spectrum Figure 48 Interface after building the project for 2D 3D energy mapping 36 Click Input 3D Parameter or Input Parameter on the toolbar and the interface for the parameter setting is shown in Figure 49 3D Happing Parameter Parameter Wavelength Detector Number File Path Change Fath Add Detector Result Del Detector Result Figure 49 Interface for the parameter setting Table 12 Description of the parameters of the interface for the parameter setting The interface after inputting the parameters is shown in Figure 50 Hose newProject 3D Parameter Map Project Input Dutput Mapping View Window Help LJ Ly SECUI Output Graph Select Spectrum Figure 50 Display after setting the parameters for 2D 3D energy mapping Click Simulation Start to start the mapping proc
28. e mesh in 2D Figure 65 Schematic diagram of the construction of the independent medium model in 2D Independent Media Model In this model the shapes of all of the tissues need to be described independently and all of the shapes will be integrated into a whole medium The following parameters need to be set while the user sets the medium to be this model 1 MediumShapeTetraType Set the flag of the type of the medium model as 0 2 TissueShape Set the shape of the tissue including the regular shape and triangle mesh structure 3 TissueCenter and TissueAxis Set the center of the regular shape and its half axis length TissuePath Set the file path when using the triangle mesh structure 5 OutermostTissueIndex Set the number of the outermost tissue User needs to 52 appoint which tissue shape 1s the outermost layer on the tissue list and the number starts from 1 Other shapes of tissues are required to be surrounded by this shape of tissue otherwise there would be some mistakes in the simulation It should be noted that the actual region of the outermost tissue is the part which equals to the shape of the tissue minus the shapes of the other tissues Figure 65 is the schematic diagram for the construction of the independent medium model in 2D Integral Medium Model In this model the shapes of all of the tissues are constructed with tetrahedral meshes that are then joined together The following parameters need to be set whi
29. e 0 1 x Z Detector Size mm Resolution Cancel Figure 30 Dialog box for adding the CCD detector Table 9 Description of the fiber detector parameters A RIRI sa in A PR WU AS EAR The central coordinate of the fiber detector shape along the X axis The central coordinate of the fiber detector shape along the Y axis The central coordinate of the fiber detector shape along the Z axis Half length of the fiber detector shape along the X axis Half length of the fiber detector shape along the Y axis Half length of the fiber detector shape along the Z axis Click Add Fiber and users will enter the Add Detector dialog box as shown in Figure 31 26 Add Fiber Detector Fiber Detector Parameter Detector Shape Ellipsoid we Positon mm mm AxisLength mm Figure 31 Dialog box for adding the fiber detector Click Del Detector and the optical parameters of the detector selected from the list will be deleted 5 Interface of the Simulation Property On this sub page users can set the simulation properties of the light propagation in the medium and free space as shown in Table 10 3D Parameter Setting Medium Light Source Detector Simulation Property Domain M CW Type of Forward Simulation O BLT FMT DOT Add Spectrum Del Spectrum Absorption Transmittance Cartesian Photon Density Cartesian Separation O Photo
30. e as that in Table 17 3DTDTransmittanceMesh Vertex The transmittance results on each mesh vertex in the first time segment 0 00000e 000 Same as that in Table 17 The total transmittance in the second time segment NOTE The contents in red font are the differences from those in Table 17 3 3 2 2 Absorption Results Compared to the absorption results under CW the absorption results under TD merely increase the time as shown in Table 32 Table 32 Format of the absorption results in a 3D Cartesian coordinate system under TD 63 TD 1 The total absorption in the second time segment 3DTDAbsorptionX YZ Same as that in Table 24 0 00000e 000 0 00000e 000 Same as that in Table 24 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 33 Table 33 Format of the transmittance results for the shape of a triangle mesh under TD 0 00000e 000 Same as that in Table 17 3DFDPhaTransmittanceMeshFace The phase of the transmittance on each mesh face 0 00000e 000 Same as that in Table 17 CountMeshVertex Same as that in Table 17 3DFDAmpTransmittanceMeshVertex The amplitude of the transmittance on each mesh vertex 0 00000e 000 Same as that in Table 17 3DFDPhaTransmittanceMeshVertex The phase of the transmittance on each mesh vertex 0 00000e 000 Same as that in Table 17 3 3 3 2 A
31. e excitation wavelength the quantum yield absorption factor and life time NOTE The last four parameters only belong to the fluorescence in the forward simulation of FMT 21 3D Parameter Setting Medium Light Source Detector Simulation Property Light Source with Regular Shape Ellipsoid 15 000000 60 000000 21 000000 0 000000 0 000000 0 000000 0 000000 Del Spectrum ili Light Source with Irregular Shape Triangle Mesh Shape File Path Change Path Azimuthal Angle min Azimuthal Angle max 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 25 Interface of the setting of the light source parameters Table 5 Description of the parameters of the light source with a regular shape The central coordinate of the tissue shape along the X axis Hao eng e se sae log the Xan EOS Half of the axis length of the tissue shape along the Y axis Deflection Angle Min The minimum deflection angle of the emitted photon Deflection Angle Max The maximum deflection angle of the emitted photon Internal Flag YES means the light source is inside the medium NO means the light source 1s outside of the medium 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
32. e tissue The order is the spectrum ges number absorption coefficient scattering coefficient anisotropy factor and refractive index The detector parameters and their numbers The plane that the detector is perpendicular to including XY DetectorLens VerticalPlane YZ and ZX NOTE The structural design of the detector in MOSE is shown in Figures 66 68 The center of the detector The normal vector of the detector osease 000 Theat iz ofthe decion he orderis gad wid PDekctrmesiion 00 The resolution o he deso ners teresa and 49 ImageDist The image distance of the detector aa ii ql fendmse The keywords to end the parameter file NOTE 1 File header 2 Simulation properties 3 Spectrum list 4 Light source parameters 5 Medium parameters 6 Detector parameters 7 Detector parameters 3 2 2 Description of the Light Source Medium Model Detector and Region of Interest 3 2 2 1 Light Source In the latest version of MOSE the types of light sources include three kinds shown in Table16 Table 16 can be a reference when user set the properties of the light source Table 16 Differences in the light source properties from different simulation types Forward simulation type ro Luminescence E l o E Bioluminescence Incident laser Incident laser Excitation fluorophore Emission type l l l The incident laser can be inside or outside of the n Inside the I
33. e transmittance results on the bottom 0 00000 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 20 3DCWTransmittanceLeft The total transmittance on the left side of the cube CountX CountZ The numbers of data along the 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 20 3DCWTransmittanceRight The total transmittance on the right side of the cube CountX CountZ The numbers of data along the 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 1s the same as that in Table 20 3DCWTransmittanceFront The total transmittance on the front side of the cube CountY CountZ The numbers of data along the Y axis and Z axis respectively 3DCWTransmittanceFrontYZ The transmittance results on the front side 0 00000e 000 0 00000e 000 Two dimensional matrix data the order 1s the same as that in Table 20 3DCWTransmittanceBack The total transmittance on the top side of the cube CountY CountZ The numbers of data along the Y axis and Z axis respectively 3DCWTransmittanceBack 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
34. ed outside of the medium Otherwise this will result in certain mistakes The location of the virtual detection plane is determined by the focal length the image distance and the center of the detector plane 53 Case l Diagram of the detector perpendicular to X Y Plane in 3D Case Top View A Height Width x Pa a View of the detector perpendicular to the X Y plane the normal vector of the detector is 0 Case 2 Diagram of the detector perpendicular to X Z Plane 7 Z in 3D Height Case 2 s Side Y Y X Width b View of the detector perpendicular to the X Z plane the normal vector of the detector is 0 Case 3 Diagram of the detector perpendicular to Y Z Plane in 3D Case 3 A 54 c View of the detector perpendicular to the Y Z plane the normal vector of the detector is 0 Figure 66 Structural design of the detector 3 2 2 4 Fiber Detector The structural design of the fiber detector in MOSE is shown in Figure 67 the fiber detector has two kinds of shape Users can set the detector needed in the simulation with the following parameters 1 Fiberdetectorshape The shape of the fiber detector In the current version the shape of the detector can be only set as cylinder or ellipsoid 2 FiberdetectorCenter Center of the fiber detector it determines the location of the detector 3 FiberdetectorAxis The half of axis length of the fib
35. em under CW CountA CountZ The numbers of data along the azimuth angle direction and Z axis respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order 1s the same as that in Table 20 3DCWTransmittanceTop The total transmittance on the top of the cylinder CountX CountY The numbers of data along the 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 1s the same as that in Table 20 3DCWTransmittanceBottom The total transmittance on the bottom of the cylinder CountX CountY The numbers of data along the X axis and Z axis respectively 59 3DCWTransmittanceBottomX Y The transmittance results on the bottom 0 00000e 000 0 00000e 000 Two dimensional matrix data the order 1s the same as that in Table 20 Table 24 Format of the transmittance results for the shape of a cube under CW 3DCWTransmittanceTop The total transmittance on the top of the cube CountX CountY The numbers of data along the X axis and Y axis respectively 3DCWTransmittanceTopX Y The transmittance results on the top 0 00000 000 0 00000e 000 Two dimensional matrix data the order is the same as that in Table 20 3DCWTransmittanceBottom The total transmittance on the bottom of the cube CountX CountY The numbers of data along the X axis and Y axis respectively 3DCWTransmittanceBottomX Y Th
36. er detector a b c values which correspond to the X axis Y axis and Z axis respectively determine the size of the fiber detector NOTE The resolution of the fiber detector is the same as that of the tissue The fiber detector can be only set at the inside of the outermost tissue The fiber can not intersect the light source To make the simulation more accurate compared with the real experiment a cavity tissue which has the same shape and center as the fiber detector is usually set to the boundary of the fiber detector Outermost ssue ellipsoid Wer detector Z Y Normal tissue ellipsoid Figure 67 Structural design of the detector 3 2 2 5 Region of Interest There are three types of simulation results in MOSE absorption results transmittance results and detection results The format of the first two results is in connection with the region of interest ROD and the coordinate system set The results have different formats with different settings The detection result is in connection with the detector size and resolution 55 aL Azimuth Angle X Radial Direction Figure 68 Illustration of the ROI The setting of the ROI contains two of the following 1 ROI The range of the ROI There are 4 directions in 2D such as the direction of the X axis the direction of the Y axis the radial direction and the azimuth direction respectively and there are 6 directions in 3D such as the direction of the
37. er is the same as that of the mesh vertices in the shape file of a triangle mesh CountMeshFace The number of data which is equal to the number of mesh faces 0 00000e 000 One dimensional matrix data the order is the same as that of the mesh faces in the shape file of the triangle mesh NOTE The formats of the contents in the green part of the table above are the same for all of the shapes and those in the blue part are different for different shapes The asterisk indicates the value Table 18 Format of the transmittance results for the shape of the tetrahedral mesh under CW 3DCWTransmittance The total transmittance at the current spectrum in 3D 3DCWTransmittanceTetraMesh The total transmittance at the boundaries of the triangle meshes of the medium CountMeshTetraVertex The number of data which is equal to the vertex number of the tetrahedral mesh 57 3DCWTransmittanceTetraMeshVertex 0 00000e 000 CountMeshTetraFace 3DCWTransmittanceTetraMeshFace 0 00000e 000 0 00000e 000 The transmittance result on each mesh vertex NOTE The transmittance on the inner vertex would be zero One dimensional matrix data the order is the same as that for the tetrahedral mesh vertices The data size of the triangle meshes The transmittance result on each boundary face of the tetrahedral mesh NOTE The transmittance on the inner boundary face would be zero Two dimensional matrix data The first
38. ertex vlx vly viz vertex v2x v2y v2z vertex v3x v3y v3z endloop endfacet endsolid name 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 purchasing MOSE 2 Why does the process of MOSE still reside in the task manager after closing the program This is because some amount of memory has not been released after closing MOSE and it may still reside in the task manager The process needs to be closed by the user manually in the task manager MOSE is developed for use at a research institute thus it is not perfect and we will work continuously to improve it 66
39. ess as shown in Figure 51 37 Project Input Dutput Mapping View Window Help o x IM ho Output Graph Select Spectrum 3D Mapping 21 8 Execute Time 0 d 00 h 00 m 00 s Ready NUM Figure 51 Interface for 2D 3D energy mapping The mapping result after the run is shown in Figure 52 Project Input Output Mapping View Window Help 51 Xa A 1 Output Graph CW Detector Map v Select Spectrum 620 gt Detector Num 1 Parameter Map aa nsmittance min 0 00e 000 Ready NUM Figure 52 Display of the detection result 38 amp Nose newProject 3D Photon Transmittance Map Project Input Output Mapping View Window Help LJ Ly SEGU Output Graph CW Transmittance Map Y Select Spectrum 620 v Figure 53 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 a triangle mesh For example select File Load Volume RAW IMG file and enter the parameter setting dialog box as shown in Figure 54 A detailed description of the dialog is in Table 13 39 Open RAW ING file Information Data type unsigned char 8 bits
40. eter file the absorption results the transmittance results and the detection results Project Input Output Simulation View Window Help LJ Ly 0 Ly la Ls DE Output Graph CW Transmittance Map Y Select Spectrum 4 newProject 3D Parameter Map TBR 4 newProject 3D Photon Transmittance Map Cu Figure46 Open a project NOTE Reading a larger amount of data may be time consuming The program state after reading is determined by the recording in the project file For example if only the parameters are inputted into 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 is done and the results have been outputted users can observe the results obtained from last run directly after opening the project at this time 35 2 3 Energy Mapping From 2D to 3D It can build a map from 2D photographic images to a 3D spatial distribution on the body surface In addition combined with the algorithm for solving the inverse problem based on the photon transport model we can reconstruct the spatial distribution of the optical properties of the medium or of the bioluminescent source inside of the medium Click File new or New Project on the toolbar and select 2D 3D energy mapping as shown in Figure 47 yject2D 3D Energy lapping JE LL QUE Output Graph Select Spectrum New Project Proje
41. ium contains only one tissue and heterogeneous medium contains more than one tissue Parameters used to define the tissue consist of the shape and optical parameters The shape can be 18 regular 2D rectangle ellipse 3D cube ellipsoid cylinder or irregular triangle mesh The optical parameters of the tissue consist of the absorption coefficient scattering coefficient anisotropy factor and refractive index As shown in Figure 21 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 In addition the refractive index of the ambient can be set at the bottom of the medium interface Ambient Refractive Index 3D Parameter Setting Medium _ Light Source Detector Simulation Property a Load File Medium Data Type Regular Shape Triangle Mesh Tetrahedron Tetrahedron Medium File Tissue with Regular Shape Tims tos ints Jones tows Foo w e wo mo wo ow Add Spectrum Del Spectrum Tissue with Irregular Shape Triangle Mesh Tetrahedron Optical Parameter Wavelengh nm Absorption 1 mm Scattering 1 mm Refractive Index Ambient Refractive Index Add Tissue Figure 21 Interface of the setting of the tissue parameters Table 2 Description of the
42. l 2 2D Cartesian Polar The coordinate system for saving the transmittance results It s related to the shape of the outermost tissue The program will automatically modify the wrong setting of the coordinate system NOTE For the Cylinder shape there are two choices for the coordinate system including the Cartesian and Cylindrical ones However there is only one choice for other shapes such as an ellipse Polar rectangle Cartesian ellipsoid Spherical cube Cartesian and triangle mesh 47 TO ows FluenceRate The flag whether or not to calculate the internal fluence rate based on the photon density Raw absorption There is only one type of data that can be saved in each simulation PhotonFlyTime The flag whether or not to record the fly time of the transmitted photons under TD OutermostTissueIndex AmbientMediumR 0 Domain CW CW There are no more parameters that need to be set TD In addition to the above parameters that need to be set the parameters related to time also need to be set The order is Tmin Tmax and Dt which correspond to the minimum time the maximum time and the time interval respectively Unit ps FD Under FD users still need to set the modulating frequency Unit MHZ MediumShapeTetraType The flag of the medium shape is 1 for a tetrahedral mesh structure and O for others endSimulationProperty
43. l field Over the past twenty years optical molecular imaging has attracted more and more attention and made progress with a series of breakthroughs The imaging technologies can be divided into two groups the first 1s 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 problem is to reconstruct the optical properties of the inner tissues or the light sources There are three distinct technology domains for optical tomography which are 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 in small animal imaging non contact imaging approaches in free space were introduced recently compared to the traditional method using light guiding fibers Although non contact imaging has become mainstream it needs to consider the procedure of light propagation in free space and makes light propagation research in this 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 Chine
44. l pop up as shown in Figure 22 Click Del Tissue and the shape parameters and optical parameters of the tissue selected in the list will be deleted Shape Type Triangle Mesh off ply surf Figure 22 Selection dialog box of the tissue shape After selecting the type of shape users will enter the interface shown in Figure 23 or 24 Figure 23 shows the added interface of the tissue with a regular shape corresponding to Tables 2 and 4 Figure 24 shows the added interface of the tissue with an irregular shape corresponding to Tables 3 and 4 20 Add Tissue Tissue Parameter Name Is Outermost NO v Shape Ellipsoid b Center Position mm Half Axis mm Optical Parameter Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refr Add Tissue Is Outermost File Path Optical Parameter Wavelengh nm lt m Figure 24 Dialog box for adding a tissue with an irregular shape 3 Light Source Interface The page for setting a light parameter is the same as that for a tissue in a specific structure as shown in Figure 25 The first list displays the parameters corresponding to the light source with a regular shape the second list displays the parameters corresponding to the light source with an irregular shape and the last list displays the optical parameters of the light source selected including the photon number the energy of the spectrum th
45. le the user sets the medium to be this model 1 MediumShapeTetraType Set the flag of the type of the medium model as 1 2 MediumTetraPath Set the file path of the tetrahedral mesh describing the whole medium the file format of the tetrahedral mesh structure refers to Section 3 4 TissueCenter TissueAxis TissuePath and OutermostTissueIndex don t need to be set otherwise this may result in some mistakes 3 2 2 3 Plane Detector The structural design of the plane detector in MOSE is shown in Figure 66 there are three designs Users can set the detector needed in the simulation with the following parameters 1 VerticalPlane Vertical plane of the detector In the current version the detector cannot be placed randomly Its detection plane must be perpendicular to the XY plane XZ plane or YZ plane shown in Figure 66 2 DetectorCenter Center of the detector plane it determines the location of the detector 3 DetectorNormal Normal vector of the detector plane the values are 0 0 and 0 which correspond to the XY plane XZ plane and YZ plane respectively Here can be any value The value determines the detection direction of the detector the correct direction points to the media from the detector plane Otherwise the detection result would be zero NOTE When setting the location of the detector the user needs to ensure that the virtual detection plane corresponding to the detection plane is locat
46. ly 2DCWAbsorptionX Y The absorption results 0 00000e 000 0 00000e 000 Two dimensional matrix data the order 1s the same as that in Table 20 Table 28 Format of the absorption results in a 2D Polar coordinate system under CW CountR CountA The numbers of data along the radial direction and azimuth angle direction respectively 0 00000e 000 0 00000e 000 Two dimensional matrix data the order 1s the same as that in Table 20 3 3 1 3 Plane Detector Results The format of the plane detector result is shown in Table 29 Table 29 Format of the detection results under CW 3DTotalDetection The number of the detector and total detection at the current spectrum HeightResolution WidthResolution The numbers of data along the directions of the height and width respectively 61 The detection results Two dimensional matrix data the order is the same as that in Table 20 3DDetectionMatrix 0 00000e 000 0 00000e 000 3 3 1 3 Fiber Detector Results The format of the fiber detector results is shown in Table 30 Table 30 Format of the fiber detection results under CW 3DCWFiberDetectorSide The detection of the detector on the side when the shape of the detector is cylinder CountA CountZ The numbers of data along the azimuth angle direction and Z axis respectively on the side 3DCWFiberDetectorSideAZ Two dimensional matrix data the order is the same 0 00000e 000 0 00000e 000 3DC
47. m will return a warning if there is failure View View Window Help we Toolbar w Status Bar Select Plane Backzround Color Color Bar Render Method Projection r F F0 F F Toolbar Set whether or not you want to display the function button bar Status Bar Set whether or not you want to display the function button bar Select Plane Select Flane x y plane Tx plane x7r plane zx plane e yz plane y plane Set the coordinate system of the view including XOY YOX XOZ ZOX YOZ and ZOY Background Color Set the background color of the view area There are three colors to choose from including black white and gray Color Bar There are five options to choose from as shown in Figure 5 including Jet Autumn Spring Hot and Cool 4 x JEJ a as Project Input Output Simulation Window Help Y Toolbar i Lay Lal MI Lal Cae Laa stein Ber Select Plane Background Color gt v Jet Output Graph CW Absorption Maj Render Method Projection Spring Hot Viewing Options Cool Figure 5 Setting the color bar w Based on vertex Based on mesh The render method includes point based and face based options The point based one adopts Render Method interpolation processing In the surface based one each face has a single color Figure 6 and 7 shows the effect of the two kinds of render methods Bose newrroject 3D Photon Ira
48. n Fluence Maximum Minimum x axis mm Y axis mm Z axis mm Radius mm B 7 1 Azimuth Angle 1 1 Deflection Angle Time ps 10 Frequency Thread Number Figure 32 Interface for the setting of the simulation properties Table 10 Description of the simulation properties The type of the forward simulation including BLT DOT and Type of Forward Simulation FMT Users can choose any one of these for each simulation Simulation domain including CW TD and FD Users can choose Domain all of these for each simulation 2 The simulation algorithm of light propagation in the medium Medium Algorithm Type Currently the algorithms only have the variance reduction Monte Carlo VRMC l The simulation algorithm of light propagation in free space Free space Algorithm Type l l l oo Currently the algorithm is based on a pinhole projection Setting of the coordinate system 2D Polar Cartesian 3D Cartesian Cylindrical used to save the absorption results The raw Absorption absorption results can be saved as the photon density or the photon fluence and users need to choose one type Setting of the coordinate system The type of coordinate system is l correlated to the shape of the medium Currently the type will be Transmittance o l l l RO modified automatically by the program to avoid using the wrong setting Setting of the separations i
49. n ROI along different directions l including the X axis Y axis Z axis radius azimuth angle Separation l l l l l deflection angle and time Please refer to Figure 66 in Section CENA Users will enter the interface of the optical simulation shown in Figure 33 after finishing the parameter setting and clicking OK in the main interface of the parameter setting Hose newProject 3D Parameter Map gt Project Input Output Simulation View Window Help LJ Ly BW oO Wi Output Graph Select Spectrum Figure 33 Interface after completing the parameter setting 28 2 2 2 3 Start Simulation The simulation will start after completing the parameter setting and clicking Simulation Start on the menu bar or toolbar as shown in Figure 34 The running time and the percentage are shown on the progress bar which is used as a reference Project Input Qutput Simulation View Window Help Lad Ld B hid Las be LY ES Output Graph Select Spectrum gt Part 1 2 Optical simulation in medium 11 0 Execute Time 0d 00h 00 m 17 s Ready NUM Figure 34 Interface for running the optical simulation In the meantime users can click the shortcuts on the toolbar or select Simulation Stop on the menu bar to stop the running operation thus the simulation will end in failure Output Graph Select Spectrum 1 Sorry Simulation is failed _ Ready NUM 29 Figure 35 Interfa
50. n of the tetrahedral mesh 13 Arich image display mainly includes 1 The display properties of the tissues can be set independently including color transparency solid wireframe display and whether or not to use a display 2 There are two ways to show simulation results absorption and transmittance results Point rendering based and surface rendering based 3 It can display multiple layers parallel to the XY YZ or XZ plane of the absorption results simultaneously which is helpful for users to quickly analyze the simulation results 14 Support the input and output of the parameter and result files under various types of simulation All of the files are managed by the project file MSE 15 Add Plane Detector and Fiber Detector 1 4 Install and Uninstall System requirements Windows 2000 XP Vista 7 or Ubuntu 10 04 10 10 Install Download the latest version of MOSE from http www mosetm net MOSE is green software no installation is required and it can be used directly after decompression User needs to choose the correct version 32 Bit or 64 Bit according to the system 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 indepe
51. ndently 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 2D detection results captured by CCD to the 3D surface of the heterogeneous medium 3 Image Processing Contains threshold extraction of raw CT data mesh simplification and boundary extraction of the tetrahedral mesh As shown in Figure 1 there are two options including New Project or Open Project which can be chosen after MOSE is started New Project Build a new project object as shown in Figure 2 The purpose of building the project is to facilitate unified management of the data related to the simulation Each individual project corresponds to a separate folder Project name and project path are set freely by the users After clicking 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 errors Open Project Open an existing project object including various data generated by the simulation as shown in Figure 3 amp Hose Project View Help OU BWEBOCOUDUOBOED E Figure Start MOSE Hew Project
52. nside or outside the l o Position l l medium The fluorophore must be inside the medium medium l medium Yes can be set while Specular the incident laser is Yes can be set while the incident laser is outside reflectance outside of the of the medium medium Solid Face Not limited Not limited Not limited Including central Including central The spectrum parameters of the incident Spectrum wavelength wavelength spectrum laser include central wavelength spectrum parameters spectrum energy energy and photon energy and photon number and photon number The spectrum parameters of the fluorophore 50 number include emission wavelength excitation wavelength quantum yield absorption factor and fluorescence lifetime Unit ps 3 2 2 2 Medium Model In the latest version of MOSE the medium is divided into two types homogeneous medium contains one tissue and inhomogeneous medium contains more than 2 tissues In the previous versions all of the tissues in the medium are independent where the boundary of the tissue can be described by regular shape or irregular triangle mesh the shapes are shown in Figure 64 a b c respectively this kind of medium model is called the Independent medium model After version 2 2 MOSE introduces a new structure of the irregular tetrahedral mesh to describe the whole medium In this structure the shapes of all of the tissues are constructed with the tetr
53. nsmittance Hap x y SETE qP Project Input Dutput Simulation Window Help e X Y Toolbar Lind Led MI Lal Lay La a Bar gt Output Graph CW Transmittance eee 620 Background Color Color Bar Projection Based on mesh Viewing Options If o fif 2 3JDeC UU J UUU Figure 6 Point based rendering Project Input Output Simulation Window Help 8 x v Toolbar L Ld MI La La Ld y Stats tor Select Pl gt Output Graph CW Transmittance lies 620 Background Color gt Color Bar Based on vertex Projection Viewing Options 2 o0e U03 003 Je t UUU Figure 7 Surface based rendering Projection Set the projection method in 3D including the perspective projection and orthographic projection The effects are displayed in Figures 8 and 9 respectively lam x lt gt Project Input Output Simulation Window Help q x Y Toolbar Lay Load KI Lal Lay La stots gt Select Pl elec ane 620 Output Graph CW Transmittance Background Color Color Bar Render Method O E ee Y Perspective Projection Orthographic Projection Viewing Options 004 min 0 00e 000 Figure 8 Perspective projection 10 x JE Oy rts Project Input Output Simulation Window Help a Y Toolbar lay Ld MI L Lay Laa Stet Be Select Plane Background Color Color Bar Render Method Output Graph CW Transmittance 620 re US Perspective Projection Viewing Options
54. nter of the shape NOTE Do not need to set it while the shape is a triangle mesh LightSourceAxis Half of the axis length of the shape NOTE Do not need to set it while the shape is a triangle mesh see Figures 63 and 64 for more information LightSourcePath The path of the triangle mesh file used to describe the irregular shape NOTE Need to set it while the shape is a triangle mesh LightSourceSpectrumInde The optical properties of the light source 5 1 Non Fluorophore the order is a spectrum number spectrum energy and photon number Fluorophore the order is a spectrum number excitation wavelength quantum yield absorption factor and fluorescence lifetime Unit ps 0 360 LightSourceAzimuthAngl The range of the azimuth angle of the emitted photon The e maximum range is 0 360 LightSourceDeflectionAn 0 180 The range of the deflection angle of the emitted photon The gle maximum range is 0 180 5 Medium TetraPath Tissue TissueShape TissueCenter TissueAxis File path of the tetrahedral mesh while the medium is a tetrahedral mesh structure The tissue parameters and their numbers Set the shape of the tissue The center of the shape Half of the axis length of the shape see Figures 63 and 64 for more information TissuePath The path of the triangle mesh file used to describe the irregular shape TissueSpectrumIndex The optical parameters of th
55. on Fiber detection figure under CW users can select the spectrum from the drop down box Select spectrum 620 and select the Detector Num detector number from the drop down box and the order of the numbers will be in accordance with the order of the detectors in the parameter file as shown in Figure 38 x o x gt Project Input Output Simulation View Window Help Output Graph CW Detector Map Select Spectrum 620 Detector Num 2 1 90e 002 min 0 00e 000 Ready HUM 31 Figure 38 fiber detector figure Output CW TD FD Absorption Map Shows the photon absorption figures under CW TD and FD 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 a single layer display and the dialog box controls when to use a multilayer display Figures 39 42 depict the results when using a Cartesian coordinate system Figures 43 45 show the results when using the Cylindrical coordinate system The detailed description of these dialog boxes are shown in Table 11 Absorption Map Setting Single layer Multilayer Single layer Setting Setting Select Spectrum 620 Select Spectrum Plane Setting Plane Setting CO xY Plane CO xY Plane Total number 0 CO Y Z Plane Total number 0 SSS CI X Z Plane Total number 0 Com Seperate the numbers with space C Y Z Plane
56. rd simulations in optical molecular imaging BLT DOT and FMT The simulation algorithms are based on the MC method 2 Support three kinds of simulation modes CW TD and FD 3 Support the description of the medium with a regular shape ellipse rectangle under 2D regular shape ellipsoid cylinder cube under 3D and irregular shape the boundary is described by a triangle mesh for example data in PLY OFF SURF MESH and AM formats and it s helpful for the users to implement the MC simulation under a complex medium Support the simulation of light propagation in free space to the panel detector such as CCD under CW The algorithm is based on the theory of pinhole imaging and Lambert s cosine law Nn Support the simulation of light propagation in medium to the fiber endoscopic detector under CW Support the function of mapping the 2D detection results from a multi angle to the 3D gt surface of the complex medium 7 Support Windows and Linux systems 8 Support multi thread optical simulation using the OpenMP API 9 Absorption results can be saved as photon absorption or photon flux density 10 Support threshold extraction of the medical image data Users can extract the boundaries of different organs based on the threshold setting the data can be used in the MC simulation 11 Support simplification of the trianglar mesh where it can reduce the mesh number effectively 12 Support boundary extractio
57. rum 620 Loading Project Loading project settings and parameters CANO NUM Figure 15 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 16 shows the interface after users choose the optical molecular imaging project under a 3D environment and click OK Bose newPro ject1i 3D Optical olecular Imaging 2 Nose inewProj ptica r zing x ES Oy Project Input Qutput Simulation View Window Help ar ara Output Graph Select Spectrum 620 Figure 16 Interface of the optical molecular imaging project under a 3D environment 15 2 2 2 2 Input Simulation Parameters Input parameters have the same steps in both a 2D and 3D environment We only discuss the 3D environment as an example Select the Input 3D Parameter and the Parameter settings dialog box pops up as shown in Figure 17 The dialog box has four different sub pages Medium Light Source Detector and Simulation Property There are two ways to set the simulation parameters Parameter file input and dialog box input They are described separately below NOTE After updating to version 2 2 the support of the tetrahedral structure data is added which is propitious to the comparison between MOSE and the finite element method However optical simulation only supports the way that a parameter file i
58. s inputted while the medium is constructed by a tetrahedral mesh in version 2 2 30 Parameter Setting Load File Medium Data Type gt d Regular Shape Triangle Mesh O Tetrahedron Add Spectrum Tetrahedron Medium File EEE Tissue with Regular Shape Tissue Nono Index Outernost Shape X om T Gn Z 600 a Gon b om Gd Tissue with Irregular Shape Triangle Mesh Tetrahedron Tissue Hane Index Outernest Shape File Path Change Path Optical Parameter Ambient Retractive Inde Figure 17 Main interface of the parameter setting 2 2 2 2 1 Parameter File Input Click Load File import the simulation parameter file from the external shown as Figure 18 MOSE sets a fixed format for the parameter file while users need to set the parameter file according to the file format requirements For a specific parameter file format see Chapter 3 After loading the parameter file users can still modify the parameters in the Parameter Setting dialog box The page of the medium properties will be different based on the differences in the medium model 1 After loading the Independent medium model regular shape or triangle mesh the media properties page 1s shown in Figure 18 a 2 After loading the Integral medium model tetrahedral mesh the media properties page 16 ID P is shown in Figure 18 b irameter Light Source Detector Simulation Property Medium
59. se Academy of Sciences China and Virginia Tech Wake Forest University School of Biomedical Engineering amp Sciences USA MOSE is featured by implementing the simulation of near infrared light propagation both in a medium with complicated shapes such as a mouse and in free space Up until now MOSE has accomplished simulation of light propagation both in a medium and in free space under CW TD and FD thus it is a powerful tool to solve the forward problems in DOT FMT and BLT This manual will help users learn how to use MOSE and more detailed information will be introduced in the following sections The solution of the inverse problem remains under investigation and will be added in a future version 1 2 New Features Compared to the previous version 2 2 the updates for version 2 3 are as follows 1 Add support to the simulation of fiber optic endoscope at the inner tissue 2 Add some new parameters and the version of the parameter file has been updated to 2 3 The latest version still supports the older versions of the parameter file 3 Change the way of output of the detector result under CW simulation First output the result of the plane detector followed by the result of fiber detector Fix the errors of the simulation property input dialog 5 Fix some other errors enhance the stability of the software to run and improve the efficiency of the algorithm 1 3 Feature List of Version 2 3 1 Support three kinds of forwa
60. side and bottom of the cylinder hence the results on the side of the cylinder are always saved following the Cylindrical coordinate system For the triangle mesh or the tetrahedral mesh the value does not need to be set for either one of them The output order of the transmittance is in accordance with the order of the mesh vertices and the mesh faces 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 56 3 3 1 CW 3 3 1 1 Transmittance Results The format of the transmittance results is recorded according to the shape of the outermost tissue The format is shown in Table 17 while the shape is a triangle mesh and the formats corresponding to the other shapes are listed in Tables 17 24 Table 17 Format of the transmittance results for the shape of the triangle mesh under CW SpecularReflectance The specular reflectance of the light sources at the current spectrum 3DCWTransmittance The total transmittance at the current spectrum in 3D 3DCWTransmittanceMesh The total transmittance of the triangle meshes CountMeshVertex The number of data which is equal to the number of mesh vertices 3DCWTransmittanceMesh Vertex 0 00000e 000 One dimensional matrix data the ord
61. te system Frequency Domain Absorption Map Setting Amplitude Setting Single layer Multilayer Select Spectrum 620 vij Plane Setting CI x Y Plane Total number 0 CI Y Z Plane Total number 0 _ X Z Plane Total number 0 Seperate the numbers with space b Multilayer display setting Absorption Map Setting Single layer Multilayer Single layer Setting Setting Select Spectrum 620 J Select Spectrum Plane Setting Plane Setting LIX Y Plane L X Y Plane Total number 0 L C Parallel to Z Axis O Parallel to Z Axis Total number 0 x Z Plane X Z Plane otal numbe ed Separate the numbers with space a Single layer display setting b Multilayer display setting Figure 43 Settings for the absorption figure under CW using a Cylindrical coordinate system Time Domain Absorption Wap Setting Time Domain Absorption Map Setting x Select the number of time Select the number of time 4 Single layer O Multilayer Single layer Setting Setting Select Spectrum 620 Select Spectrum 620 Plane Setting Plane Setting C x Y Plane C1 XY Plane Total number 0 C Parallel to Z Axis C Parallel to Z Axis Total number 0 Total number Separate the numbers with space X Z Plane X Z Plane a Single layer display setting b Multilayer display setting
62. three lines are the vertex number of the triangle mesh on the boundaries of the medium including the inner boundary and outer boundary the last line is the transmittance result of each triangle mesh Table 19 Format of the transmittance results for the shape of the rectangle under CW 0 00000e 000 One dimensional matrix data 2DCWTransmittanceDown 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 The number of data along the Y axis 2DCW TransmittanceLeftY The transmittance results on the left side 0 00000e 000 One dimensional matrix data 2DCWTransmittanceRight The total transmittance on the right side of the rectangle The number of data along the Y axis 2DCWTransmittanceRightY The transmittance results on the right side 0 00000e 000 One dimensional matrix data Table 20 Format of the transmittance results for the shape of an ellipse under CW 2DCWTransmittance 2DCWTransmittanceSide CountA 2DCWTransmittanceSideA 0 00000e 000 The total transmittance at the current spectrum in 2D The total transmittance on the side of the ellipse The number of data along the direction of the azimuth angle The transmittance results on the side One dimensional matrix data Table 21 Format of the transmittan
63. ting the medium interface the light source interface the detector interface and the interface of the simulation properties 1 Main Interface of the Parameter Setting Click Add spectrum where users can add a new spectrum as shown in Figure 19 Due to the different optical parameters among different spectra users should enter the optical parameters of the tissues and source parameters corresponding to the new spectrum Add Spectrun Wavelength Tissue Optical Parameter Tissue Name Absorption 1 mm Scattering 1 mm Anisotropy Refractive Index PhantomSur face Light Source Optical Parameter Number of Photons Spectrum Energy Excitation Wav Quantum Yield AL Figure 19 Dialog box of adding a new spectrum Click Del Spectrum users can delete the selected spectrum shown as Figure 20 Click OK and all of the optical parameters of the tissues and the source parameters corresponding to the spectrum will be deleted DelSpectrun Choose Spectrum Figure 20 Dialog box of deleting a spectrum Click Apply and users will save all of the parameters in the interface Click Cancel and users will quit the Parameter Setting dialog box without saving the parameters Click OK and users will save all of 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 a homogeneous med
64. tion The function of boundary extraction from the tetrahedral mesh can be used to obtain the boundary data of the tetrahedral mesh For example the tetrahedral mesh can be formed after tetrahedralization of the complex region and can be used in the finite element method The boundary extraction can be used to obtain the triangle mesh boundary of each region from the tetrahedral mesh Select File Load Surface MESH AM File after reading the tetrahedral data files in a mesh or am format All of the internal and external boundaries of the tetrahedral mesh are shown in Figure 61 43 A a MS Simplification Map gt File Mesh Simplification Segmentation Mesh Extraction View Window Help GG KG ls 6 E E ES Figure 61 Reading the tetrahedral data After reading the tetrahedral data select Mesh Extraction Tetrahedron Boundary Extraction and the dialog box shown in Figure 62 will pop up a Ss A Pe Seg Aaf y pepa B Cancel Ready NUM Figure 62 Tetrahedral boundary extraction After selecting the file storage path from the dialog and clicking the OK button it starts extracting the tetrahedral regional boundaries from the tetrahedral data and saves it as a grid file in the off format The surface and liver of the digimouse are extracted and shown in Figure 63 44 amp Hose newProject Image Processing rs File Mesh Simplification Segmentation Mesh Extraction View Window Help JG iS Es
65. transmittance results under FD in results under FD an MC simulation The file of the detection results Save the detection results under CW in an under CW MC simulation The file of raw data The input data in threshold segmentation The file of triangular data Triangle mesh data which can be used to describe the tissue shape in an MC simulation The file of triangular data Triangle mesh data which can be used to describe the tissue shape in an MC simulation The file of triangular data Triangle mesh data which can be used to generated from Netgen describe the tissue shape in an MC simulation The file of tetrahedral data Tetrahedral mesh data which can be used generated from Amira to describe the integral structure of the medium in an MC simulation The file of tetrahedral data Tetrahedral mesh data which can be used generated from Netgen to describe the integral structure of the medium in an MC simulation 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 15 Format specification of the parameter file A ri File type pe Format ASCII 2 0 ASCII encoding version 2 0 corresponding to MOSE v2 1 2 A 2 SimulationProperty WA The keywords to start the setting of the simulation property Comment This file is generated by MOSE SimulationType Dimension BLT The forward simulation type BLT

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