User`s Manual Release 2.0
Contents
1. 4 000000 Wavelength Number of Photons Source Energy center y mm 6 000000 620 3500 1 000000 000 center z 7 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER PE a 0 500000 b mm 0 500000 nm L c 0 500000 distribution Uni form Cancel Q tissue Conc Parameter Figure 12 6 Set the property of the light source c CCD List All the detectors are shown on the upper list corresponding information including position and shape parameters which can be modified are shown in the second list Right click a certain detector we could add or delete a detector or set the parameters of lens see Figure 12 7 Figure 12 8 Figure 12 9 17 DetectorLen 1 DetectorLen 2 Add cco Del CCD Lens DetectorLen 1 DetectorLen DetectorLen 3 DetectorLen 4 data center x mm 0 000000 center y mm 12 000000 center z mm 0 000000 shape CUBE alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 a mm 10 000000 b mm 0 000000 mm 11 000000 Save Matrix Tes Coordinate System Cartesian E dx mm 0 200000 dy mm 0 200000 dz 0 200000 Parameter data center x mm 0 000000 center y mm 0 000000 center z mm 0 000000 shape CUBE ie alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 a mm 0 000000 b mm 0 000000 c m2. Browse Add Spectrum Optical Parameter of PhantomSurface Del Spectrum Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refractive 0 008761 20 973200 0 940000 1 350000 0 005012 20 454500 0 940000 1 350000 Apply Cancel Add Tissue Del Tissue OK Figure 7 2 Input dialog box for parameter of tissues in 3D mesh The Optical Parameter list shows the optical parameters of the tissue which is chosen in the Tissue list in each spectrum band including absorption coefficient scattering coefficient refractive index and anisotropy coefficient Notice Since the first tissue represents the phantom it cannot be deleted And other tissues must be in the range of the phantom Otherwise errors would happen during simulation Add Tissue Tissue Parameters Center Position Tissue Name Tissue Shape Rotation Angle Optical Parameter W avelenah Absorption 1 Scattering 1 Anisotropy Refractive Cancel Figure 7 3 Dialog box for adding a new tissue a Click the button Add Tissue an input dialog box will be shown as Figure 7 3 We can add tissue we need Here we should input the tissue s name shape center coordinates rotation angle half axis length and optical parameters Especially in 3D mesh environment we need to input the path of the ply off files see Figure 7 4 Click the OK button the new tissue will be ad
3. es Mose 3D Mouse Phanton 4 f wt Ec t ip 3 Sy Data Original Map Figure 13 Simulation is over a Output of Simulation Parameter Select menu Simulation parameter under Output menu we can save the parameters including the tissues the light sources the detectors and the simulation parameter for MC in the form of the standard parameter file mse file which will be saved into the current project folder for simulation in future b Output of simulation results for Monte Carlo 20 Select menu 3D Analytic Absorption Result under Output menu we can save the absorption matrix of the Monte Carlo simulation to the current project folder Select menu 3D Analytic Transmittance Result under Output menu we can save the transmittance matrix of the Monte Carlo simulation to the current project folder c Output of 3D CCD Result Select menu 3D CCD Result under Output menu we can save the detection matrix of the Monte Carlo simulation to the current project folder Notice The results of the different spectrum bands of absorption results are output into the same file the transmittance and detection results are also too d Output of 3D Flee Map Select menu 3D Flee Map under Output menu or Flee Map in the first drop down list box on the toolbar we can see the Flee Map of this simulation And we can select the spectrum band in the following drop down list box See Figure 14 1 amp am
4. 0 000000 center 0 000000 center z 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER 10 000000 b mm 10 000000 11 000000 ccn Figure 11 Interface of simulation in 3D analytic environment In this image white represents tissues red represents light source and gray is CCD Unfolding the sidebar we can find the parameters of tissue light source CCD and MC inputted These parameters can be modified easily and flexibly here a Tissue list Tissue name is shown in the upper list corresponding information including position and shape parameters which can be modified are shown in the second list in 3D mesh environment the second list shows the path of the ply off file We can add tissue delete tissue or set the optical parameter by right clicking the tissue name see Figure 12 1 Figure 12 2 Figure 12 3 14 PhantomSurface Heart LeftKidney Del Tissue Optical Parameters data center x mm 5 000000 center y mm 0 000000 center mm 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape ELLIPSOID a mm 4 000000 b mm 5 000000 c mm 7 000000 Qeon Qc Farante Add Tissue Tissue Parameters Center Position Tissue Tissue Shape s Rotation Angle Alpha zz Beta 0 0 Gamma Optical Paramete
5. 005 1 38401 005 1 43259 005 data of the matrix 24 Appendix D FAQ 1 Why the display of the phantom stay unchanged after the parameters have been modified in the sidebar Answer After modify the parameters in the sidebar clicking the save button on the toolbar will save the parameters meanwhile updating their display 2 What is the meaning of different types of absorption matrix and transmission matrix in the MC Simulation Parameter page of the input parameter dialog box Answer The absorption matrix has two forms of cartesian coordinate and cylindrical coordinate The difference between them is to define the position of photon be absorbed in cartesian coordinate or cylindrical coordinate The different choice of coordinate system will lead to different absorption matrix visual effect The cartesian coordinate form absorption matrix will display in form of slice of absorption matrix parallel to X Y plane The cylindrical coordinate form absorption matrix will display in form of slice of absorption matrix parallel to Z axis Slices need to be observed can be chosen by glide bar The amount of absorb is represented by color But corresponding color bar 1 not been displayed yet According to different simulation environment absorption matrix has different type It only has polar coordinate form in 2D simulation environment but has cartesian coordinate form and cylindrical coordinate form in 3D analytic mesh
6. 002 12315e 002 18169 002 18119e 002 98502 002 77375 002 3315Te 002 33097 002 44774 002 68799 002 97743 002 67993 002 59133 002 28390e 002 38146e 002 64365 002 89247 002 37517 002 44 1 1 Ch 6533Te 002 95952e 002 45284e 002 10104e 002 94068e 002 11902e 002 09835e 002 25535e 002 16546e 002 54890e 002 10967 002 86734e 002 16880e 002 12311e 002 4 00 4 4 1 CO OOo OQ 4 68148e 002 02507 002 50071 002 33816e 002 18089e 002 00808 002 55155e 002 58401 002 56179 002 21581e 002 11438e 002 15934e 002 07065 002 4836Te 002 47553 002 37581 002 18405 002 12816 002 88087 002 29118 002 57063 002 36254 002 61395 002 36163 002 55976e 002 13230e 002 60212 002 90184e 002 25 spectrum 620 center wavelength of the spectrum 3DTransmittanceSide 8 89940 00 the total energy Watt of corresponding spectrum band countA countZ 360 20 the size of the matrix The unit of the matrix is W mm in 2D while is W mm in 3D environment 3DtransmittanceSideAZ 7 19233 002 7 00232 002 6 30366e 002 6 98502e 002 6 65337e 002 7 68149e 002 7 47553 002 7 08378e 002 6 55314e 002 8 05368e 002 7 46624e 002 6 86954 002 7 42
7. The steps of inputting the parameter in the three simulation environments are similar Here we just take the 3D analytic environment as the example See Figure 3 2 in the main window under the input menu click 3D Analytic Parameter or click the button ed The Input Parameters window appears See Figure 5 There are four different input pages named Tissue Light Source CCD and MC simulation respectively 3D Analytic Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter Tissue Load Data Parameter X mm Y mm Z mm Shape Alpha degree Belta degree Gamma degree xm alia Optical Parameter Wavelengh nm Absorption 1 mmy Scattering 1 mm Anisotropy Refractive Add Tissue Del Tissue Figure 5 Input dialog box for simulation parameters a Click button Load Data we can load 3D analytic parameter file mse txt from outside We provide some file examples for user to study how to use MOSE If the form of the file 1 not correct only the correct parameters will be read in and other parameters need to be input manually After loading data the parameter will be seen in the Input Parameters dialog box b Click the button Add Spectrum we can add new spectrum band as Figure 6 1 indicates Also the optical parameter of all the tissues in the new spectrum band should be set in this dialog box The information of the light sources in t
8. detector will be set to zero a Click the button Add CCD a new row for detector would be added into the CCD list And the corresponding parameters information can be input by user b Click the button Del CCD the selected detector and its information would be deleted 5 Page of Monte Carlo MC parameter The information about absorption matrix and transmittance matrix for Monte Carlo simulation is illustrated in this page Figure 10 including the coordinate system and resolution of the absorption matrix and transmittance matrix We can choose whether to save the two matrixes or not 3D Analytic Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter Absorption Matrix coordinate system Cylindrical iv save Load Data Add Spectrum Transmittance Matrix Del Spectrum coordinate system Cylindrical save Resolution x axis 0 1 mm y axis 0 1 mm z axis 0 1 mm polar radius 0 3 mm polar angle 1 degree Apply Cancel 13 Figure 10 Input dialog box for MC simulation parameter 6 Modification of the parameter in sidebar When the parameters in four pages are all inputted click the button OK then enter the simulation interface shown in Figure 11 8 Mose 3D Mouse Phantom d gt Fie Input Output Simulation View Window Help ze PhantomSurface Heart LeftKidney RightKidney Bone data center x
9. environment Transmission matrix has polar coordinate form in 2D simulation environment cylindrical coordinate form in 3D analytic environment cartesian coordinate form in 3D analytic and mesh environment 3 When the program is running why clicking the left key of mouse is ineffective to restore up a minimized program window Answer You can restore up the window by clicking the restore menu on the taskbar 4 In the 3 D mesh simulation environment what are the meanings of the 3DTransmittanceMeshFace and the 3DTransmittanceMeshVertsx respectively Answer 3DTransmittanceMeshFace represents the emitted flux density w mm of each triangular mesh face 3D TransmittanceMesh Vertex represents the emitted flux density w mm of each triangular mesh vertex The former is the ratio between the total weight of photons that emitted from the triangular mesh face and the area of the triangular mesh the later 15 the ratio between the total energy and total area of triangular mesh which exists the intersectant parts of the point and the order of the results of the 3DTransmittanceMesh Vertex conforms to that of the vertexes of the outer tissue of the phantom 25 5 The progress bar would shade image of the original simulation data and make the user couldn t observer the data how to handle this problem Answer When the MOSE running the progress bar is in the center of the window of MOSE all the time and can t be mov
10. 0 000 00000 000 00000 000 000002 000 the center wavelength of spectrum band 00000 000 00000 000 00000 000 00000 000 00000e 000 00000e 000 00000e 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 000002 000 the total energy in corresponding spectrum band Watt countR 11 countA 360 countZ 23 the size of the absorption matrix The unit of the matrix is W mm in 2D while 15 W mm in 3D environment 3DAbsorptionRAZ 0 00000 000 0 00000 000 0 00000 000 0 00000 000 0 00000 000 0 00000 000 0 00000 000 0 00000 000 0 00000 000 0 00000 000 data of the matrix 2 The file of the transmittance result Spectrum 620 3DTransmitt anceSide 8 89940e 001 countA countZ 360 20 3DTransmittanceSideAZ 1 19233e 002 7 00232 002 6 59276e 002 52075 002 6 66025 002 5 T5769e 002 6 93954 002 6 43372 002 T 14180e 002 T 24055 002 6 66815 002 6 91224e 002 6 27886 002 92126 002 7 29741 002 6 46770 002 20905 002 6 68235 002 20941 002 T 63066e 002 87945 002 20770 002 89946 002 6 37282 002 07722 002 6 13928 002 84467 002 51462 002 30366e 002 13248e 002 66038e 002 4418Te 002 53469e 002 86219e 002 67275 002 70363 002 36440e 002 14933 002 31344e
11. 000000 Cylinder 0 000000 0 000000 Del Spectrum Optical Parameter of PhantomSurface Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refractive 0 008761 20 973200 0 940000 1 350000 Apply Cancel Add Tissue Del Tissue Figure 7 1 Input dialog box for tissue parameter X x coordinates of the center location of the tissue Y y coordinates of the center location of the tissue Z z coordinates of the center location of the tissue Alpha the rotation angle of the tissue shape with respect to x axis Beta the rotation angle of the tissue shape with respect to y axis Gamma the rotation angle of the tissue shape with respect to z axis a the length of half axis of x coordinate b the length of half axis of y coordinate c the length of half axis of z coordinate Shape the geometric shape of the tissue Where MOSE provides two kinds of shape model Ellipse Rectangle in 2D environment and Ellipsoid Cylinder in 3D environment Especially in 3D mesh environment tissue shape consist of triangle mesh structure such as ply off files see Figure 7 2 3D Mesh Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter Tissue Parameter Shape File Path Change Path Phantoms c cylinder_surfa Browse c ellipsoid_heart Browse LeftKidnev c ellipsoid_leftki Browse RightKidnev c Vellipsoid right Browse c icylinder_bone
12. 054 002 6 82968 002 6 59465 002 7 60552e 002 7 38552e 002 6 44916e 002 data of the matrix 3 The file of detector result Spectrum 620 3DDetection 1 1 49110e 002 countY countZ 100 110 3DDetectionYZ 8 2984Te 006 8 55013 006 8 81174 006 9 08377 006 8 36672e 006 9 66114e 006 9 96756e 006 8 32638e 006 8 57958 006 8 84282 006 9 11660 006 9 40143 006 9 69783e 006 1 00064 005 8 2835Te 006 8 53645 006 8 79942 006 9 07299 006 9 35765 006 9 65396 006 9 96249 006 8 19424 006 8 44561 006 8 70708 006 8 97914 006 9 26232 006 9 5571 006 9 86426 006 8 13566 006 8 38635 006 8 64716 006 8 91859 006 9 20117 006 9 49546 006 9 80206 006 8 15282 006 8 40450 006 8 66637 006 8 93894 006 9 22274 006 9 51835 006 9 82635 006 8 16722e 006 8 41975e 006 8 68253 006 8 95608 006 9 24093 006 9 53767 006 9 84687 006 spectrum 620 center wavelength of spectrum 3DDetection 1 The Num 1 is the serial number of the CCD 1 49110e 002 the total energy Watt in corresponding spectrum band absorbed by CCD 1 CountY CountZ 100 110 the size of the matrix The unit of the matrix is W mm in 3D environment 3DDetectionYZ 8 29847e 006 8 55013 006 81174e 006 9 08377 006 9 36672 006 9 66114 006 9 96756e 006 1 02866e 005 1 06188e 005 1 09650e 005 1 13257 005 1 17017 005 1 20938 005 1 25029e 005 1 29296e 005 1 33751
13. MOLECULAR IMAGE GROUP LIFE SCIENCE RESEARCH CENTER XIDIAN UNIVERSITY XIAN MEDIAL IMAGE PROCESSING GROUP INSTITUTE OF AUTOMATION CAS BEIJING P R C VT WFU SCHOOL OF BIOMEDICAL ENGINEERING amp SCIENCES VIRGINIA U S A MOSE Molecular Optical Simulation Environment User s Manual Release 2 0 Service e mail mose life xidian edu cn Rn ee ee 2 MOSE csc A A 2 How input the 2 How does MOSE 2 Can run MOSE on my 2 3 Getting started with MOSE 3 Step T ecce REA P RU RI RR 3 Step 2 Parameter InDUE oo oe hoe ete to Rot a V 6 Step 3 Simulation and Output of MOSE 20 APPENA emm ODORE 23 CETUS IS ssa ss sacs cca een vanes noosa NM IE 23 ET CC cC 25 geo TEE 25 Appendix What is MOSE MOSE is a photon tracing program for optical analysis of biological tissue models MOSE traces photons using Carlo Technique The best way to describe how MOSE works might be to briefly outline the st
14. d at the bottom of the Tissue list ESSE Tissue Mame Shape File Path Browse Optical Parameter Wavelengh nm Scattering 1 mrmn Anisotropy Refractive Cancel Figure 7 4 Add Tissue dialog box in 3D mesh b Click the button Del Tissue delete selected tissue and its optical parameters 3 Page of Light Source parameter This page consists of the information of regular shape light sources Figure 8 1 Similar to the tissue page the upper list shows the information of the light sources including the center coordinates shape rotation angle half axis length and the form of energy distribution 3D Analytic Simulation x Tissue Parameter Light Source Parameter Parameter MC Simulation Parameter Light Source Load Data Parameter X mm Y mm 2 mm Shape Alpha degree Belta degree 0 Light source 1 4 000000 6 000000 7 000000 Ellipsoid 0 000000 0 000000 Light source 2 4 000000 6 000000 7 000000 Cylinder 0 000000 0 000000 Add Spectrum lt Property of Light source 1 Wavelenth nm NumberOfPhotons SourceEnergy W 550 1 000000 000 Add Light Source Del Light Source Del Spectrum v p dH Apply Cancel Figure 8 1 Input dialog box for light source parameter The lower list shows the information of the light source which 1 chose in the upper list including t
15. e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 0000024000 spectrum 400 3DAbosrption 2 99970e 001 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 00000 000 00000 000 00000 000 00000 000 00000 000 00000e 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 000002 000 pS Se Vm isi Se fei te leh fe 00000 000 00000 000 00000e 000 00000 000 00000 000 00000e 000 00000e 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 000002 000 Sale Le Pah tes 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 So oo gt gt gt gt oa O 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 00000 000 0000
16. ed to other places but the user could move the image of the original simulation data by the left button right button and middle button Moving the mouse after depress the left button could rotate the image or the right button could zoom in out the image or the middle button could move the image in the window 6 Why the process of MOSE still exists in the task manager when the error appears in some situation when running and the MOSE 1 closed Answer Because the MOSE is still in the development There have some bugs that can t be avoided existing in the MOSE and that can make the execution abort unexpected and this caused that the memory of the MOSE isn t released correctly So the process of MOSE still exists in the task management We would solve this problem gradually in the subsequent versions 7 In the 3 D mesh simulation environment why the error still happens in reading the simulation parameters file mse when the path of the file representing the tissue shape 1 right Answer Maybe the reason is that the path of file contains blank or some other illegal character that can t be identified by the computer You need to set the path of the shape file in the Tissue Parameter page or Light Source Parameter page 26
17. el Fig 12 9 Set the parameters of lens d MC parameter page see Figure 12 10 we can set the information of absorption and transmittance matrix in this page Mose 3D Mouse Phantom 4 Fle inf Quiet Smisen Window Help 3 Absorption Matrix coordinate system Cylindrical w save Transmittance Matrix coordinate system Cylindrical save Resolution xaxis 0 100000 mm yaxis 9 100000 zaxis 9 100000 mm polar radius 1 000000 mm polar angle 1 000000 degree Quis Oriar Que P Roady NUM Figure 12 10 Set the simulation parameter for MC e After modifying all the parameters click the button on toolbar to save them all 19 Step 3 Simulation and Output of MOSE After we finished the parameters setting click the menu Run under the menu Simulation or the button 9 on the toolbar to start simulation After the simulation is finished see Figure 13 we can choose the output we need Here in the display window Rotation and zoom in or zoom out operation of the image can be done by dragging the mouse left key and dragging the mouse right key respectively And dragging the mouse middle key could move the image Other buttons are as follows Ww the button to fold unfold the sidebar e the button to switch the display form of the phantom wireframe or flat shaded 2 the button to reset the coordinate axis
18. eps that are typically taken if you were to start a new MOSE project These steps will be discussed in greater depth in the following sections 1 Parameters The first step is to build a geometrical model representing the system you wish to analyze During this operation you need to input both the geometric and optical properties of the tissue 2 Simulation This second step is to run the system you defined above 3 Output the MOSE Once the simulation finished you can find the output of MOSE including absorption map flee map and CCD map You can also save the simulation parameters absorption results and transmittance results In MOSE for consistency we use millimetre mm as the basic unit of length throughout the whole software How do input the parameters MOSE has a very friendly user interface And it offers two efficient approaches for us to input the parameters One is loading the parameter files mse file which has a specified form We will offer some standard parameter files to the users to study how to construct the parameter file The other is inputting the parameters in the parameter setting dialog box No matter which approach you can simply modify parameters after inputting You can add or delete tissues or light sources or detectors if you need This is especially useful when the kinds of tissues or light sources or detectors are more than the default settings How doe
19. he photon energy and photon number of the light source in different spectrum band Here if the light source doesn t include one of the spectrum bands 10 corresponding photon number and energy should be set to zero Especially in 3D mesh environment there re two kinds of shape of the light source One is analytic shape ellipsoid cylinder the other is mesh shape mctrian glemesh The upper list mentioned above 1 divided into two lists Figure 8 2 The Analytic Light Source list shows the light sources which are of analytic shape while the Mesh Light Source list shows the light sources which are of mesh shape 3D Mesh Simulation Tissue Parameter Light Source Parameter ccD Parameter MC Simulation Parameter Analytic Light Source Parameter X mm Y mm 2 mm Shape Alpha degree degree Light source 1 4 000000 6 000000 7 000000 Cylinder 0 000000 0 000000 Load Data Add Spectrum Mesh Light Source Parameter Shape File Path Change Path Light source 2 2 Browse Del Spectrum Apply Property of Light source 1 NumberOfPhotons 500 500 SourceEnergy W 1 000000e 000 1 000000e 000 Wavelengh nm Add Light Source Del Light Source Cancel 0 te fi Figure 8 2 Input dialog box for parameter of light sources in 3D mesh environment a Click the button Add Light Source regular shape light
20. his spectrum band could be set in Light Source Parameter Page Notice In MOSE we take the center wavelength to represent the spectrum band Add Spectrum Wavelength nm Tissue Optical Parameter tissue Absorption 1 Scattering Anisotropy Refractive RightKidne Cancel Figure 6 1 Dialog box for adding spectrum band c Click the button Del Spectrum choose the spectrum band that we want to delete as Figure 6 2 indicates and press Button OK to delete it After this step the tissues parameters and the light sources parameters related to this spectrum would be deleted Dels pectrum Choose Spectrum Figure 6 2 Dialog box for deleting a spectrum band d Click button Apply all the parameters in the pages will be saved 2 Page of Tissue parameter See Figure 7 1 The Tissue list of this page shows the parameters of all tissues including the center coordinates shape rotation angle half axis length 3D Analytic Simulation issue Load Data Parameter mm Y mm 2 mm Shape Alpha degree degree _ PhantomSurface 0 000000 0 000000 0 000000 Cylinder 0 000000 0 000000 0 000000 4 000000 6 000000 Ellipsoid 0 000000 0 000000 LeftKidney 5 000000 0 000000 0 000000 Ellipsoid 0 000000 0 000000 RightKidney 5 000000 0 000000 0 000000 Ellipsoid 0 000000 0 000000 Add Spectrum 0 000000 5 000000 0
21. ight source or set the energy distributing and the number of photons in each spectrum band see Figure 12 4 Figure 12 5 and Figure 12 6 Add Light Source Add Light Source Light sour Del Light Source Property Light Source Parameter Light Source Shape Light Source Distribution Center Position Rotation Angle Figure 12 4 Add a light source Shape Parameter Alpha 0 center x 4 000000 b center 6 000000 center 2 7 000000 0 ES alpha degree 0 000000 belta degree 0 000000 Property gamma degree 0 000000 Wavele NumberOfPhotons SourceEnergy shape CYLINDER B a mm 0 500000 b mm 0 500000 c 0 500000 distribution Uni form E 16 Mose 3D Mouse Phantom File Input Output Simulation View Window Help amp B Wwe S Light source 1 Add Light Source Del Light Source Property Parameter data center x 4 000000 center y mm 6 000000 center z mm 7 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER a mm 0 500000 b 0 500000 c 0 500000 distribution Uni form Q tissue Quia Qc Parameter Ready Figure 12 5 Delete a light source Light source 1 Light 5 add Light Source Del Light Source Property Light Source Property X data center x
22. m 0 000000 Save Matrix Tes E Coordinate System Cartesian E dx mm 0 100000 dy mm 0 100000 dz 0 100000 Fig 12 7 Add a CCD detector Q tissue Parameter Mose 3D Mouse Phantom File Input Output Simulation View Window Help e lt rm 1 DetectorLen 1 DetectorLen 2 Add CCD Dete 77 Detet Lens Parameter data center x 12 000000 center y 0 000000 2 0 000000 shape CUBE alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 0 000000 b 10 000000 11 00000 Save Matrix Tes E Coordinate System Cartesian dx mm 0 200000 dy mm 0 200000 dz 0 200000 Q tissue Quia Parameter Ready Fig 12 8 Delete a CCD detector 18 DetectorLen 1 DetectorLen 2 YES Len Shape Ellipsoid Focus 5 data Center Position Rotation Angle center mm 12 000000 EM Alpha 0 center y mm 0 000000 center z mm 0 000000 Belta shape CUBE B alpha degree 0 000000 Hamma 0 belta degree 0 000000 gamma degree 0 000000 Siue Pa ram CET iru a mm 0 000000 b mm 10 000000 11 mm 0 mm c mm 11 000000 Save Matrix Tes B 13 mm y Coordinate System Cartesian E dx mm 0 200000 2 dy mm 0 200000 dz mml 0 200000 IEEE IMMINENTE eee Cancel tissue Farametet Canc
23. nvironment 3D analytic environment and 3D mesh environment The different simulation environment has different type of phantom After this step MOSE will display different interface according to your choice Figure 3 1 Figure 3 2 and Figure 3 3 shows the interface of 2D 3D analytic and 3D mesh environment respectively Mose 2D Monte Carlo Simulation 4 File Input Output Simulation View Window Help T Figure 3 1 Default interface of 2D simulation environment T File Input Output Simulation View Window Help A 5 e File Input Output Simulation Mesh Simplification Segmentation View Window Help Figure 3 3 Default interface of 3D mesh simulation environment 3 Open a project You can open the project you have simulated before Select the Open menu under the File menu or click the button toolbar and find parameter file mse you have saved last time MOSE will automaticlly select simulation environment and show the image of the phantom according to the parameter file Figure 4 EU 30 Mesh Mouse Phantom e File Input Output Simulation Mesh Simplification Segmentation View Window Help BAUS E Gg PhantomSurface LeftKidney RightKidney Bone E SS SS ZFS D mose Param 57 Figure 4 Open a project that is in 3D mesh environment Step 2 Parameter Input 1
24. p Mose 3D Photon Flee Map E File Input Output Simulation View Window Help e lt Flee Map 1620 Figure 14 1 in 3D analytic environment Output of 3D CCD Map Select menu CCD Map under Output menu or CCD Map in the first drop down list box on the toolbar to show the map on CCD In the following drop down list box we can choose the spectrum band The serial number of CCD Map is consistent with the sequence of detectors which can be changed through the glide bar see Figure 14 2 21 Figure 14 2 CCD map in 3D analytic environment f Output of 3D Absorption Map Select menu Absorption Map under Output menu or Absorption Map in the first drop down list box on the toolbar to show the Absorption Map of the simulation We can choose the spectrum band in the following drop down list box The display of the absorption maps here is layered Absorption Map of a certain layer can be shown by dragging the slider of the glide bar see Figure 14 3 gt File Input Output Simulation View Window Help 2 W d Absorption ka x Figure 14 3 Absorption map in 3D analytic environment 22 Appendix Output Results 1 The file of the absorption result spectrum 400 3DAbsorption 75 99970 001 11 countA 360 countZ 3DAbsorptionRAZ 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000e 000 0 00000 000 0 00000
25. r Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refractive 620 Figure 12 1 Add tissue Mose 3D Mouse Phantom e File Input Output Simulation View Window Help amp bah WV E PhantomSurface Heart LeftKidney Add Tissue ou Optical Parameters Parameter data 5 000000 0 000000 0 000000 0 000000 center center center z alpha degree belta degree 0 000000 gamma degree 0 000000 shape ELLIPSOID 4 000000 b 5 000000 7 000000 tissue Oii Parameter Ready Figure 12 2 Delete a tissue 15 Add Tissue Del Tissue Optical Parameters Optical Parameter Parameter center x mm 5 000000 z center 0 000000 Wavelength Absorption 6 Scattering Anisotropy Refractive center z mm 0 000000 0 154980 18 092400 0 860000 1 370000 alpha degree 0 000000 belta degree 0 000000 0 000000 shape ELLIPSOID a mm 4 000000 b 5 000000 mm 7 000000 Drissue Quiz Geen LOC Parameter Figure 12 3 Set the optical parameters of the light source b Light list Light source 15 shown in the upper list corresponding information including position and shape parameters which can be modified are shown in the second list Right click a certain light source we can add or delete a l
26. s MOSE simulate The whole propagation of each photon packet includes three main parts photon packet generation from bioluminescent sources the propagation in biological tissues and detection by the CCD detectors which was completed through the Monte Carlo MC method The MC method has been proved to be exact and efficient During the whole process MOSE not only traces the travel paths of each photon packet but also records the absorption and transmittance information Through these records MOSE can give the absorption and flee map of the photons phantom Can run MOSE my computer Until now MOSE can run on Microsoft Windows 98 2000 NT XP Vista Appendix Getting started with MOSE Step 1 MOSE 1 Double click the MOSE exe file and Monte Carlo simulation application software will start immediately Figure 1 Mose File View Help VES Figure 1 Main Window of MOSE 2 The first step to start the simulation is to build a new project Select the menu named New under the File menu or click the button on the toolbar the New Simulation Project window appears Figure 2 New Simulation Project Project Name Path Selected Environment 2D Simulation 3D Analytic Simulation 3D Mesh Simulation cnet Figure 2 Build a New Project Input your project name select the save path through and the simulation environment There are three environment in MOSE 2D e
27. source will be added and the input dialog box is as follows Figure 8 3 Add Light Source Light Source Parameter Light Source Shape Light Source Distribution 7 Center Position Rotation Angle Shape Parameter Cancel Figure 8 3 Dialog box for adding a light source 11 Where we should set shape form of energy distribution center coordinates rotation angle half axis length of the light source and photon number and energy in corresponding spectrum band Especially in 3D mesh environment we should select the shape type before we input the parameters of the light source see Figure 8 4 and Figure 8 5 Light Source Shape Analytic Shape Mesh Shape Figure 8 4 Dialog for selecting the shape type Add Light Source Source Parameter File Path Property Wavele NumberOFPhabons SourceEnergy 620 650 Figure 8 5 Add Light Source dialog box if select mesh shape b Click the button Del Light Source the selected light source and its parameters would be deleted 4 Page of CCD detector parameter See Figure 9 information including the center coordinates shape rotation angle half axis length resolution and normal vector of CCD the flag for detector matrix saving the coordinate system of detector matrix and the flag for lens being is shown the list of this page Where Resol
28. ution dx the resolution of x coordinate Resolution dy the resolution of y coordinate Resolution dz the resolution of z coordinate The Lens list shows the information about lens corresponding to each of the detectors including the center coordinates shape rotation angle half axis length normal vector and focus of the lens 12 3D Mesh Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter CCD Parameter X mm Y mm 2 Shape Alpha degree Belta degree Ga Load Data Detector 1 11 000000 0 000000 0 000000 Cube 0 000000 0 000000 Detector 2 11 000000 0 000000 0 000000 Cube 0 000000 0 000000 Detector 3 0 000000 11 000000 0 000000 Cube 0 000000 0 000000 Detector 4 0 000000 11 000000 0 000000 Cube 0 000000 0 000000 Add Spectrum x mm Y mm Z mm Shape Alpha degree Belta degree Gamm Del Spectrum Detector 0 000000 0 000000 3 000000 Ellipsoid 0 000000 0 000000 D C Detector2 0 000000 0 000000 3 000000 Ellipsoid 0 000000 0 000000 D C Detector3 0 000000 0 000000 3 000000 Ellipsoid 0 000000 0 000000 D C Detector4 0 000000 0 000000 3 000000 Ellipsoid 0 000000 0 000000 D C Apply Add CCD Del CCD Cancel Figure 9 Input dialog box for parameter of detectors and lens If the last item Lens item in the CCD list is set to be nolens all the lens parameters in the Lens list for the corresponding
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