User Manual Release 2.1
Contents
1. Analytic Light Source SSSL Parameter x mm Y mm Z mm Shape Alpha degree Belta dearee Load Data Light source 1 4 000000 6 000000 7 000000 Cylinder 0 000000 0 000000 Add Spectrum Mesh Light Source Parameter Shape File Path Change Path Light source 2 c 2 ply Browse Del Spectrum Appl Property of Light source 1 pply Wavelengh nm NumberOfPhotons SourceEnergy Vv 500 1 000000e 000 500 1 000000e 000 Add Light Source Del Light Source Cancel OK les t 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 source will be added and the input dialog box is as follows Figure 8 3 Add Light Source Light Source Parameter Light Source Shape Ellipsoid Light Source Distribution Uniform Kack Position i Shape Parameter i i a b C Cancel Figure 8 3 Dialog box for adding a light source Where we should set the shape the 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 11 input the parameters of the light source see Figure 8 4 and Figure 8 5 Light Source Shape Type e Analytic Shape Mesh Shape Figure 8 4 Dialog f2. 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 90000e 000 90000e 000 UUOUUetUOU 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 90000e 000 00000e 000 00000e 000 00000e 000 N0000R 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 N00N0R 000 90000e 000 00000e 000 00000e 000 90000e 000 90000e 000 00000e 000 00000e 000 00000e 000 00000e 000 90000e 000 90000e 000 90000e 000 90000e 000 90000e 000 9N000e 000 the center wavelength of the spectrum band 0 00000e 000 00000e 000 00000e 000 0 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 00000e 000 90000e 000 90000e 000 90000e 000 0N000e 000 32 2 99970e 001 countR JI countA 360 countZ 23 the size of the absorption matrix the total energy of corresponding spectrum band Watt A The unit of the matrix is W mm in 2D while is W mm in 3D environment 3DAbsorptionRAZ 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 data of the matrix 2 The fi
3. it needs to choose and create the appropriate type project on the specific function MOSE includes two different types of projects BLT and image processing You will enter in different operating interface according to the type of project The following will define the different types of projects in detail How to input the parameters MOSE has a very friendly user interface There are a number of ways to input data and output results for users Take the BLT project for example 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 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 It is especially useful when the kinds of tissues or light sources or detectors are more than the default settings How does MOSE simulate After inputting the parameters we can start the BLT simulation or the image processing Take the BLT project for example Monte Carlo MC method constructs the foundation of the BLT and in the MC method the source was discretized into a number of photon packets The whole propagation of each photon packet includes three main parts photon packet generation from bio
4. A Zs t Lu 19 3 111 219 SRD RN 12 9 6 4 min 0 00e 000 Figure 14 6 Single absorption map vertical to z axis in cylindrical coordinate Select Multiple layers the absorption map will be displayed in Multiple layers model Set layers in the dialog box w with the space between them then the absorption maps of the layers are appeared shown in figure 14 7 14 8 14 9 14 10 Similar to Slice plane Absorption Hap Setting Single layer setting Select spectrum 620 Slice plane xy plane yz plane x z plane Total number of the slices 219 Input the number of the slices you need 20 7099110 150 180 210 Apply Seperate the numbers with space Figure14 7 Interface of setting multiple layers absorption map in cartesian coordinate 26 Absorption Map Setting C Single layer Kdultiple layers setting Select spectrum 620 slice plane e along z axis Perpendicular to z axis Total number of the slices 99 Input the number of the slices you need 2 15 48 76 35 Apply Seperate the numbers with space Figure14 8 Interface of setting multiple layers absorption map in cylindrical coordinate Ze Nose 123 3D Photon Absorption Map g File Input Output Simulation View Window Help Ae e WVvoGis Output graph Absorption Map Select spectrum Absorption Map Setting C Single layer Multiple layers Setting max 3 87e 002 Select spectrum 6
5. point and the order of the results of the 3DTransmittanceMesh Vertex conforms to that of the vertexes of the outer tissue of the phantom 5 The progress bar would shade the 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 moved 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 depressing 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 1s closed Answer Because the MOSE is still in the development It have some bugs that can t 35 be avoided in 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 is right Answer Maybe the reason is that the path of fil
6. related to this spectrum will be deleted DeGpectrum 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 As in figure 7 1 The Tissue list of this page shows the parameters of all tissues including name center coordinates shape rotation angle half axis length 3D Analytic Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter Tissue Parameter X mm 7 mm Gen TERE ey rg Load Data PhantomSur face 0 000000 0 000000 0 000000 Cylinder 10 000000 10 Heart 0 000000 4 000000 6 000000 Ellipsoid 4 000000 2 0 LeftKi dney 5 000000 0 000000 0 000000 Ellipsoid 4 000000 4 0 Add Spectrum Ri ghtKi dney 5 000000 0 000000 0 000000 Ellipsoid 4 000000 5 0m lt gt Del Spectrum Optical Parameter of PhantomSurface Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refrac 620 0 008761 20 973200 0 940000 1 350 gt 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 angl
7. the current project folder c Output of 3D Flee Map Select menu Flee Map under Output menu or select Output graph FleeMap 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 spectrum 620 in the following drop down list box See Figure 14 1 22 ATAT L Output graph Flee Map Select spectrum 620 PhantomSurface Heart LeftKidney RightKidney Bone Parameter Data center x mm 0 000000 center y mm 5 000000 center z mm 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER Se a mm 1 000000 b mm 1 000000 c mm 10 000000 Figure 14 1 Flee map in 3D analytic environment d Output of 3D CCD Map Select menu CCD Map under Output menu or select Output graph 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 sPectum 620 The drop down list box CCP Num Detector2 select the serial number of detector the order of the serial number is same as the detector in input parameters see Figure 14 2 23 a Hose 123 3D Analytic Photon CCD Map d File Input Output Simulation View Window Help K Zb GL SN CSATA AA A Output graph CCD Map si Select spectrum 620 CCD Num Detector3 x PhantomSurface Heart LeftKidney RightKidney Bone Parameter
8. to start simulation After finishing the simulation 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 d Y the button to fold unfold the sidebar 21 9 the button to reset the coordinate axis Hose 123 3D House Phantom dh Yv Abwwewvo s Output graph Data Original Map Select spectrum PhantomSurface Heart LeftKidney RightKidney Bone Parameter Data center x mm 0 000000 center y mm 4 000000 center z mm 6 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape ELLIPSOID x a mm 4 000000 b mm 2 000000 2 000000 Qi ssue Li ght 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 standard parameter file mse file which will be saved into current project folder for simulation in future b Output of simulation results for Monte Carlo Select menu 3D Simulation Result under Output menu the absorption matrix transmittance matrix and detection matrix of the Monte Carlo simulation could be saved to
9. your project name select the save path through MOSE will create a new folder under the path and the folder include a mp file Note In the project of the type of BLT the information of tissues light sources etc and the simulation results could be saved in the file folder And this information is related by a project file In the project of image processing the information is not related because there is no such absolute relationship between image process and output data Where the user must select save path to avoid some errors caused by inputting path hand manual As shown in figure 2 we can select simulate project pattern in item of project according to different pattern MOSE can appear different interface At present MOSE include two kinds of project BLT and image process Where BLT includes three kinds of environment 2D environment 3D analytic environment and 3D mesh environment Image processing includes threshold segmentation and mesh simplification 3 Open a project Users can open a project built previously The type of mp and other associated file could also be open And the interface would show the corresponding state according to the parameters of the project file Taking the BLT project as example if the simulation had been run and the files of parameters and results had been output in the previous project these files of parameters and results would be opened together when the project was opened And it may tak
10. z Select spectrum 620 Light source 1 ENUE Add Light Source Del Light Source Property center x mm center y mm center z mm alpha degree belta degree gamma degree shape a mm b mm c mm distribution 4 000000 6 000000 7 000000 0 000000 0 000000 0 000000 CYLINDER v 0 500000 0 500000 0 500000 Uni form Qrissue Qua Qcc Cu Parameter Ready Figure 12 5 Delete a light source 17 Light Source Property Wavelength t Number of Photons Source Energy 220 1 000000e 000 A7 WW zo Light Source oe pe Light Source Property pn Cancel 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 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 DetectorLen 1 DetectorLen 1 ATT DetectorLen 2 Add TCD i DetectorLen 3 aT 7 DetectorLen 3 DetectorLen 4 DetectorLen 4 Lene S DetectorLen 5 center x mm 0 000000 center x mm 0 000000 center y mm 12 000000 center y mm 0 000000 center z mm 0 000000 center z mm 0 000000 shape CUBE shape CUBE alpha degree 0 000000 alpha degree 0 000000 belta degree 0 000000 belta degree 0 000000 gamma degree 0 000000 g
11. 0 1 mm z axis 0 1 mm polar radius 0 1 mm polar angle 1 degree Cancel Figure 10 Input dialog box for MC simulation parameter 6 Modification of the parameter in sidebar After the parameters in four pages are all inputted click the button OK then enter the simulation interface shown in Figure 11 Hose 123 3D Mouse Phanton d File Input Output Simulation View Window Help SHARE Output graph Data Original Map gt Select spectrum 620 PhantomSurface Heart LeftKidney RightKidney Bone center x mm 0 000000 center y mm 0 000000 center z mm 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER X a mm 10 000000 b mm 10 000000 c mm 11 000000 i Q Tissue QLiert Ocen Quc Parameter Ready Figure 11 Interface of simulation in 3D analytic environment 14 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 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 Figur
12. 20 kee 1e 003 Slice plane Q EES SO 32 2 C along z axis Perpendicular to z axis gt 58 center x i center center Input the number of the slices you need 105080110150 180 210 Apply o A Wek yj 12 9 Total number of the slices 219 19 3 Seperate the numbers with space 6 4 min 0 00e 000 Figure 14 9 Multiple absorption map vertical to z axis in cylindrical coordinate 2 CS Hose 123 3D Photon Absorption Map lt File Input Qutput Simulation View Window Help i 3 CD a AA oe AS WWWVSoOE Output graph Absorption Map si Select spectrum Light source 1 Absorption Map Setting C Single layer Multiple layers max 3 82e 002 1e 00 Setting 31 8 Paramete Select spectrum 620 center x Zi Ca al AN center y Slice plane 25 4 center z x y plane C y z plane x z plane 19 0 Total number of the slices 219 Input the number of the slices you need 12 7 10 50 80 100 111 150 180 210 rane QQ SPREE Ka Seperate the numbers with space min 0 00e 000 Qrissue Ready Figure 14 10 Multiple absorption map parallel to xy axis in cartesian coordinate 2 Image Processing Project When image processing was chosen the corresponding interface appears which includes two functions Threshold Segmentation and Mesh Simplification a Mesh simplification and Output Results Select Input Load Data ply file load ply or off file outside shown in figure 1
13. 5 1 after loaded 28 zs Nose 1234 Image Processing 4 File Mesh Simplification Segmentation View Window Help apdQoonmr SE NY ee ani Kan 4S D AN ECKE SNE PEK e E 2 gt WA ie ay Figure 15 1 Display after load ply file Select Mesh Simplification QEM Arithmetic the dialog box of mesh simplification pops up Then we can set the target number of mesh then the result is shown in figure 15 3 Set Face Humber Current Num Taget Num 200 SS Figure 15 2 Dialog for mesh simplification 29 e Mose 1234 Image Processing d File Mesh Simplification Segmentation View Window Help aD OQO0OM Figure 15 3 Result of mesh simplification Select Output Mesh Simplification Result the simplified results will be saved in the file of ply b Threshold Segmentation and Output Results Select Input Load Data raw file load raw file outside a parameter setting dialog for file inputting pops up as shown in Figurel6 1 Then click the button OK the interface appears if file is correctly inputted shown in Figure16 2 Open KAN file Filename a Information Width 600 Pixel interval 0 053 mm Height 596 Pixel interval 0 053 mm Number of see 2 Slice interval ear mm Number of channels ee Data type unsigned char 8 bits Head length O ResolutionAngle Ce ResolutionXYZ IS mm Cancel Figure 16 1 Dialog for parameter setting 30 Ss Hose 1234 Threshold Seg
14. Cptical Parameters EI Cancel Figure 12 3 Set the optical parameters of the light source b Light list Light source is shown in the upper list corresponding information including position and shape parameters which can be modified in the second list Right click a certain light source we can add or delete a light source or set the photon energy distributing and the number of photons in each spectrum band see Figure 12 4 Figure 12 5 and Figure 12 6 16 Add Light Source Light sour De Light Source Property Parameter Data center x mm 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 ELLIPSOID mm 2 000000 b mm 1 000000 c mm 1 000000 i distribution Uni form Display Setting Light source 1 S amp __ 6 8 36 Opacity j 20 Show F Solid display Qtissue Qi v Gw Paraneter Add Light Source Light Source Parameter Light Source Shape Light Source Distribution Center Position Rotation Angle x mm Alpha y E mm Belta a 0 mm Gamma Property Wavele NumberOfPhotons SourceEneray 620 Cylinder Ellipsoid 0 0 0 Shape Parameter mm J cnet Figure 12 4 Add a light source Hose 123 3D Mouse Phantona de File Input Qutput Simulation View Window Help Ee Data Original Map
15. D Analytic Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter Tissue Parameter Add Spectrum Del Spectrum Optical Parameter Wavelengh nm Absorption 1 mm Scattering 1 mm Apply Cancel Add Tissue Del Tissue OK Figure 5 Input dialog box for simulation parameters a Click the 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 is not correct only the correct parameters will be read in and others 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 could be set in this dialog box The information of the light sources in this spectrum band could be set in Light Source Parameter Page Add Spectrum Wavelength nm Tissue Optical Parameter tissue Absorption 1 mm Scattering Lim Anisotropy Refractive PhantomSt 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
16. Data center x mm 0 000000 center y mm 0 000000 center z mm 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER a mm 10 000000 b mm 10 000000 11 000000 i Tissue QL ght Figure 14 2 CCD map in 3D analytic environment e Output of 3D Absorption Map Select menu Absorption Map under Output menu or select Output graph 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 spectrum 620 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 It has two different maps map in cartesian coordinate and in cylindrical coordinate Figure 14 3 14 4 Absorption Hap Setting C Multiple layers Select spectrum 620 Slice plane C xy plane C y z plane x z plane Select the number of slice _ _ 8 Figure 14 3 Interface of setting absorption map in cartesian coordinate 24 Absorption Map Setting Single layer Multiple layers Setting Selectspectrum 620 M Slice plane along z axis Perpendicular to z axis Select the number of slice Hmmm n Figure 14 4 Interface of setting absorption map in cylindrical coordinate Select Single layer the absorption map is displayed in single layer model select Select the number of sli
17. MOLECULAR IMAGE GROUP LIFE SCIENCE RESEARCH CENTER XIDIAN UNIVERSITY XIAN P R C 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 Manual Release 2 1 Service e mail mose life xidian edu cn PAD DCT e EE 2 HERE EOCUUS EE 2 How to input the DE HEES 2 How does MOSE simulate o oo ccccsccccesssceceessseeceesseeeceesseeceesseeeeessseeeesaeees 2 Can I run MOSE on my computer 3 D v lopment LAN GQUAGC ee 3 Compilation Environment sic isso cis cn eek ee ee 3 APPENA B EE 3 Getting started with MOSE eiert 3 1 Molecular Imaging rot eendeitege edel 4 Step 1 Get into the Simulation Environment 5 Step 2 HEET eebe eieiei 6 Step 3 Simulation and Output Of MOGSE cess eeeneeeees 21 2 Image Processing Project 28 VV 9 lt 1 Le b EE 32 The Format of Output Results 2 000000 ccc ccccsssccceessseceesseeeeessseeeeenseeceesaeees 32 ADDeENdIX RE 34 Ee 34 Appendix A Introduction MOSE is a photon tracing program for optical analysis of biological tissue models MOSE traces photons using Monte Carlo Technique The best way to describe how does MOSE work might be to briefly outline the steps that are typically taken if you were to start a new MOSE project These steps will be discussed in the following sections If you are beginning to create a new MOSE project
18. amma degree 0 000000 a mm 10 000000 a mm 0 000000 b Imm 0 000000 b mm 0 000000 c mm c mm Save Matrix Tes Save Matrix Yes Coordinate System ertesi an Coordinate System Cartesian dx mm 0 200000 dx mm 0 100000 dy mm 0 200000 dy mm 0 100000 dz mm 0 200000 dz mm 0 100000 normal vector x 0 000000 normal vector x 0 000000 normal vector y 1 000000 normal vector y 0 000000 normal vector z 0 000000 normal vector z 0 000000 Display Setting DetectorLen 2 H el 255 R J 255 G _ _ 255 G 255 Be j 255 B 255 Opacity 38 E Show V Show Display Setting DetectorLen 5 Opacity __ 20 Tissue GA i Figure 12 7 Add a CCD detector ccr 18 Hose 123 3D Mouse Phanton lt gt File Input Qutput Simulation View Window Help SUP WVOOE Output graph Data Orginal Map Select spectrum 620 DetectorLen 1 Detecto Add CCD Lens center x mm 0 000000 center y mm 12 000000 center z mm 0 000000 shape CUBE alpha degree belta degree gamma degree a mm 0 000000 0 000000 0 000000 10 000000 b mm 0 000000 c mm 11 000000 Coordinate System Cartesian dx mm 0 200000 dy mm 0 200000 dz mm 0 200000 normal vector x 0 000000 normal vector y 1 000000 normal vector z 0 000000 Qrissue QL zht Ac nc Parameter Ready DetectorLen 1 DetectorLen 4 Parameter Len
19. arameter for MC e After modifying all the parameters click the button z on the toolbar to save them all f Display Setting a function to display various attributes of protracted object is set in the area of the sidebar in each simulation environment when left key strike on the corresponding object this area will be the setting of display property of the selected object see figure 12 11 20 Leirkid nrw Hieabuikidncsw Bone Data 0 00000 4 000000 0 000000 0 000000 O 000000 ree 000000 R jerm si 3 000000 1 500000 6 000000 Display Setting Le kidney 255 255 D d 255 arx w Show Solid displiy i Geen Ce Ferescter Figure 12 11 Set the simulation parameter for MC R 1_ 255 J 255 Display Setting LeftKidney e e i Where A i represents the object selection Di 255 represents the setting of color red green and blue of the selected tissue source or CCD SE 80 is used to set the clarity of the object the bigger w Show Solid display percentage the more opaque the object is is used to determine whether to display the object and select the display state in closed or solid This Display Setting function is also available in the tissue light and CCD interface Step 3 Simulation and Output of MOSE After we finished the parameters setting click the menu Run under the menu Simulation or the button V on the toolbar
20. ce layers in the glide bar 4 77 In cartesian coordinate X Y option means layer selection is paralleling x y axis so Y Z Z X means the selection paralleled y z and z x axis in the same way Selecting the option along z axis means that the mode of layer selecting is spar sampling paralleled to z axis selecting the option Perpendicular to z axis means that the mode of layer selecting is ellipsoidal sampling vertical to z axis Here there are two kinds of absorption maps one if them is paralleling to x y axis in cartesian coordinate and the other is vertical to z axis in cylindrical coordinate Figure 14 5 14 6 ABD WWW OOE FT Output graph Absorption Map Select spectrum x Light source 1 Absorption Hap Setting e Single layer C Multiple layers max 3 82e 002 1e 003 Setting 31 8 Select spectrum 620 D Slice plane 25 4 e x lane C yz plane C x z plane Y p yz p p 19 0 Select the number of slice K N 12 7 1117219 6 3 distributi min 0 00e 000 Qrissue Ready Figure 14 5 Single absorption map parallel to xy axis in cartesian coordinate 25 Nose 123 3D Photon Absorption Map AS CWVoOEr Output graph Absorption Map l Select spectrum Absorption Hap Setting Single layer C Multiple layers Setting max 3 67e 002 Select spectrum 620 E 1e 003 Slice plane 32 2 C along z axis Perpendicular to z axis D5 8 Select the number of slice ID
21. e 12 1 Figure 12 2 Figure 12 3 PhantomSurface Add Tissue center x mm 0 000000 center y mm 4 000000 Tissue Parameters center z mm 6 000000 alpha degree 0 000000 belta degree 0 000000 i RR gamma degree 0 000000 Tissue Name shape ELLIPSOID ER a mm 4 000000 s i T b mm 2 000000 Tissue Shape Z soid c mm 2 000000 Ellipsoid Center Position r Rotation Angle Shape Parameter X Oar Alpha 0 a op y Omm Belta b i z 0 mm Gamma 0 c 0 mm Display Setting Heart Optical Parameter H A Wavelengh mm Absorption Scattering Anisot Refr G j 25 8 j 255 Opacity ir 80 Show F Solid display unt Figure 12 1 Add a tissue 15 Hose 123 3D Mouse Phantom Input Output Simulation View Window Help ABePLDVSOOE Output graph Data Original Map v Select spectrum 620 PhantomSurface Lef Add Tissue ig De Tissue Boi Optical Parameters center x mm 0 000000 center y mm 4 000000 center z mm 6 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 ELLIPSOID e 4 000000 2 000000 2 000000 Otissue Ora e Cu Parameter Ready x Wavelength Absorption Scattering Anisotropy Refractive 620 0 154980 18 092400 0 860000 1 370000 PhantomSurtace Heart Add Tissue Pit el Tissue ram 4
22. e 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 36
23. e 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 under 3D mesh environment tissue shape consists of triangle mesh structure such as ply off files 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 LeftKidney c ellipsoid_leftki Browse RightKidney c ellipsoid_right Browse c icylinder_bone Browse Add Spectrum r 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 represe
24. e some time to do this procedure when loading huge data After this procedure users could observe the results got by the simulation before through the buttons on the interface 1 Molecular Imaging Project Molecular Imaging MI only includes Bioluminescence Tomography BLT at version 2 1 There will have Fluorescence Molecular Tomography FMT and Diffuse Optical Tomography DOT being added to this project in future Step 1 Get into the Simulation Environment If select built a new project choose the simulation environment in the dialog of new project and then step into the corresponding simulation interface The different simulation environment has different type of phantom After this step MOSE will display different interface according to your choice Figure 3 1 shows the interface of 2D environment Hose 123 3D Analytic Monte Carlo Simulation gt File Input Output Simulation View Window Help Abe IL P n SE a d E Output graph Select spectrum Figure 3 1 Interface of 2D simulation environment If you want to open the former project select the Open menu under the File menu or click the button Si on the toolbar and find the project file mpj file saved before the simulation environment parameter file absorption result transmittance result and CCD result would be loaded automatically in MOSE shown in Figure 4 Choosing a new project or open the old one next step will change according to the different op
25. energy Watt of 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 55013e 006 81174e 006 9 08377e 006 9 36672e 006 9 66114e 006 9 96756e 006 1 02866e 005 1 06188e 005 1 09650e 005 1 13257e 005 1 17017e 005 1 20938e 005 1 25029e 005 1 29296e 005 1 33751e 005 1 38401e 005 1 43259e 005 data of the matrix 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 only when clicking the save button on the toolbar could save the parameters meanwhile updating would be displayed 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 There are two types of absorption matrix artesian coordinate and cylindrical coordinate The difference between them is to define the position of photon be 34 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
26. enter wavelength of the spectrum 3DTransmittanceSide 8 59940e 00 the total energy Watt of corresponding spectrum band countA countZ 360 20 The unit of the matrix is W mm in 2D while is Wimm in 3D environment the size of the matrix 3DtransmittanceSideAZ 7 19233e 002 7 00232e 002 6 30366e 002 6 98502e 002 6 65337e 002 7 68149e 002 7 47553e 002 7 08378e 002 6 553 14e 002 8 05368e 002 7 46624e 002 6 56954e 002 7 42054e 002 6 82968e 002 6 59465e 002 7 60552e 002 7 38552e 002 44916e 002 data of the matrix 33 3 The file of detector result Spectrum 620 3DDetection 1 1 49110e 002 countY countZ 100 110 3DDet ectionYZ 8 29847Te 006 8 55013e 006 8 81174e 006 9 0837TTe 006 9 36672e 006 9 66114e 006 9 96756e 006 8 32638e 006 8 57958e 006 8 84282e 006 9 11660e 006 9 40143e 006 9 69783e 006 1 00064e 005 8 2835Te 006 8 53645e 006 8 79942e 006 9 07T299e 006 9 35765e 006 9 65396e 006 9 96249e 006 8 19424e 006 8 44561le 006 8 TOTO8e 006 8 97914de 006 9 26232e 006 9 55717e 006 9 86426e 006 8 13566e 006 8 38635e 006 8 64716e 006 8 91859e 006 9 20117e 006 9 49546e 006 9 80206e 006 8 15282e 006 8 40450e 006 8 66637e 006 8 93894e 006 9 222T4de 006 9 51835e 006 9 82635e 006 8 16722e 006 8 41975e 006 8 68253e 006 8 95608e 006 9 24093e 006 9 53767Te 006 9 8468Te 006 spectrum 620 center wavelength of the spectrum 3DDetection I The Num 1 is the serial number of the CCD 1 49110e 002 the total
27. for parameter of detectors and lens Where Resolution 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 If the last item Lens item in the CCD list set to be nolens all the lens parameters in the Lens list for the corresponding 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 inputted 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 13 3D Analytic Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter Absorption Matrix Load Data coordinate system Cylindrical d Add Spectrum Transmittance Matrix Del Spectrum coordinate system Cylindrical Resolution x axis 0 1 mm y axis
28. le of the transmittance result Spectrum 620 3DTransmitt anceSide 8 89940e 001 countA countZ 360 20 3DTransmitt anceSideAZ T 19233e 002 7 00232e 002 6 30366e 002 6 98502e 002 6 6533Te O02 7 68149e 002 7 47553e 002 6 59276e 002 7 52075e 002 7 13249e 002 6 77375e 002 6 95952e 002 7 02507e 002 7 37581e 002 6 66025e 002 5 75769e 002 5 66038e 002 T 33157e 002 7 45284e 002 6 50071e 002 T 18405e 002 6 93954e 002 6 43372e 002 6 44187e O002 6 33097e 002 7 10104e 002 8 33816e 002 7 12816e 002 T 74180e 002 7 24055e 002 6 53469e 002 7 44774e 002 6 94068e 002 6 78089e 002 6 8808Te 002 6 66815e 002 6 91224e 002 6 86219e 002 8 68799e 002 7 77902e 002 6 00808e 002 7 29118e 002 6 27886e 002 5 92126e 002 7 67275e 002 6 97743e 002 7 09935e 002 7 55155e 002 7 57063e 002 T 29741e 002 6 46770e 002 6 70363e 002 6 67993e 002 7 25535e 002 7 58401le 002 8 36254e 002 T 20905e 002 6 68235e 002 7 36440e 002 7 59133e 002 6 76546e 002 7 56179e 002 7 613595e 002 T 20941e 002 7 63066e 002 7 14933e 002 6 28390e 002 7 54890e 002 6 2158le 002 6 36163e 002 T 87945e 002 7 20770e 002 7 37344e 002 7 39146e 002 7 10967e O002 8 17438e 002 6 559T6e 002 T 89946e 002 6 37282e 002 7 72315e 002 5 64365e 002 7 86734e 002 7 75934e 002 8 T3230e 002 T OF 722e 002 6 13928e 002 7 18169e 002 7 89247e 002 7 76880e 002 7 07065e 002 7 60212e 002 T 84467e 002 7 51462e 002 7 18119e 002 6 37517e 002 7 72371e 002 7 48367e 002 5 90184e 002 spectrum 620 c
29. luminescent sources the propagation in biological tissues and detection by the CCD detectors which were 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 With these records MOSE can give absorption and flee map of the photons in phantom Can run MOSE on my computer Until now MOSE can run on Microsoft Windows 98 2000 NT XP Vista Development Language Kernel arithmetic was developed by C while interface development was MFC Compilation Environment VC 6 0 Appendix B Getting started with MOSE 1 Run MOSE 1 Double click the MOSE exe file and Monte Carlo simulation application software will start immediately Figure 1 Hose SE File View Help AB eRVSOEFEQVOVOCONs Output graph Select spectrum d Figure 1 Main Window of MOSE 2 New project 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 ice on the toolbar the New Simulation Project window appears Figure 2 Hew Simulation Project Project Name 123 Project Path Select Project Type f Molecular Imaging BLT Select Simulation Environment 2D f 3D Analytic C 3D Mesh C Image Processing Figure 2 Build a New Project Input
30. mentation Map gt File Mesh Simplification Segmentation View Window Help EO 0000 inv Figure 16 2 Display after input raw file Select Segmentation Threshold Segmentation the dialog box of setting threshold pops up shown in figure 16 3 After setting upper and lower threshold we will obtain the threshold segmentation result shown in figure 16 4 Set Threshold High Threshold DI Low Threshold 0 cancel Figure 16 3 Dialog for setting threshold 31 Gol Hose 1234 Threshold Segmentation Map 3 File Mesh Simplification Segmentation View Window Help 27 OCH OO Figure 16 4 Display for threshold segmentation result Select Output Segmentation Result the results of threshold segmentation will be outputted in the file of ply Appendix C The Format of Output Results 1 The file of the absorption result spectrum 400 3DAbsorption d 99970e 001 countR 11 countA 360 countZ 3DAbsorptionRAZ 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 0 00000e 000 N 00000e 000 spectrum 400 3DAbosrption 23 00000e 000 00000e 000 00000e 000
31. nts the phantom it cannot be deleted And other tissues must be in the range of phantom Otherwise errors would happen during simulation Add Tissue Tissue Parameters Center Position Ee i y 0 mm E Tissue Name Alpha 9 a In mm Belta Ia b a mm Gamma 9 E 0 mm Optical Parameter Wavelengh nm Absorption 1 mm Scattering 1 mm Anisotropy Refractive Cancel Figure 7 3 Dialog box for adding a new tissue a Click the button Add Tissue there will be an input dialog box as Figure7 3 shown We can add tissue as 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 Figure 7 4 Click the OK button the new tissue will be added in the Tissue list Add Tissue Tissue Name Shape File Path Browse Optical Parameter 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 of the light sources Figure 8 1 As 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 dis
32. or selecting the shape type Add Light Source Light Source Parameter File Path ca Fe Property Wavele NumberOfPhotons SourceEneray i Cancel Figure 8 5 Add Light Source dialog box if select the 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 in the CCD list of this page 12 3D Analytic Simulation Tissue Parameter Light Source Parameter CCD Parameter MC Simulation Parameter ccD Parameter X mm mm Z mm Shape a mm b m Detector 1 12 000000 0 000000 0 000000 Cube 0 000000 10 00C Load Data Detector 2 0 000000 12 000000 0 000000 Cube 10 000000 0 000 Detector 3 12 000000 0 000000 0 000000 Cube 0 000000 10 000 Add Spectrum lt gt Lens Del Spectrum Lens X mm Y mm Z mm Shape a mm b Inn Detectorl 0 000000 0 000000 3 000000 Ellipsoid 11 000000 13 000C Detector 0 000000 0 000000 3 000000 Ellipsoid 11 000000 13 0000 Detector3 0 000000 0 000000 3 000000 Ellipsoid 11 000000 13 000C y lt a Add CCD Del CCD Figure 9 Input dialog box
33. s DetectorLen 2 x z Ach CD DetectorLen 3 Del CCH center x mm center y mm center z mm shape 0 000000 12 000000 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 a mm 10 000000 b mm 0 000000 c mm 11 000000 1 Save Matrix Tes Coordinate System Cartesian dx mm 0 200000 dy mm 0 200000 ds mm 0 200000 normal vector x 000000 normal vector y 1 000000 normal vector z 0 000000 Display Setting DetectorLen 2 A J 255 G J 255 B 255 Opacity 701 Iw Show Tissue Lie Been Ce Paraneter Figure 12 9 Set the parameters of lens Lens Flag Len Shape Center Position Figure 12 8 Delete a CCD detector mm mm Focus e Rotation Angle Alpha Belta Gamma Kee Vector E omm y om im Cancel d MC parameter page see Figure 12 10 we can set the information of absorption and transmittance matrix in this page 19 Hose 123 3D Mouse Phantom lt q File Input Qutput Simulation View Window Help AB e WVoeoeir Output graph Data Original Map Select spectrum 620 Absorption Matrix coordinate system Cartesian D Transmittance Matrix coordinate system Cylindrical Resolution x axis 0 100000 mm y axis 0 100000 mm z axis 0 100000 mm Mi Qrissue QL i ek Cu Parameter Ready Figure 12 10 Set the simulation p
34. tion for user User will handle the Parameter Input and Simulation and Output of MOSE when you built a new project If open an old project user could do these steps selective For example if user just inputted parameters last time we should finish the Simulation and Output of MOSE 5 step if not we will restart it If all the two steps were done what we should do is just to open it and get the result Hose Kosel File Input Qutput Simulation View Window Help rw A D Son w 2 CGSMw a0Rp Output graph Absorption Map si Select spectrum CCD Num Detector4 v og 123 3D House Phantom PhantomSurface Heart LeftKidney RightKidney Bone Parameter Data center x mm 0 000000 center y mm 0 000000 center z mm 0 000000 alpha degree 0 000000 belta degree 0 000000 gamma degree 0 000000 shape CYLINDER a mm 10 000000 b mm 10 000000 c mm 11 000000 Figure 4 Open a BLT project that is in 3D mesh environment Step 2 Parameter Input 1 The steps of inputting the parameter in these three simulation environments are similar Here we just take the 3D analytic environment as the example As in Figure 3 2 in the main window under the input menu click 3D Analytic Parameter or click the button E The Input Parameters window appears See Figure 5 There are four different input pages named Tissue Light Source CCD and MC simulation respectively 3
35. to Z axis Slices need to be observed by glide bar The amount of absorb is represented by color But corresponding color bar is 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 and mesh environment Transmission matrix only 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 3DTransmittanceMesh Vertsx respectively Answer 3DTransmittanceMeshFace represents the emitted flux density w mm of each triangular mesh face 3DTransmittanceMeshVertex 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 is the ratio between the total energy and total area of triangular mesh which exists in the intersectant parts of the
36. tribution 3D Analytic Simulation Tissue Parameter Light Source Parameter ccD Parameter MC Simulation Parameter r Light Source Load Data Parameter X mm T nm Z mm Shape a mm b mn 4 000000 6 000000 7 000000 Cylinder 0 500000 0 50001 4 000000 6 000000 7 000000 Cylinder 0 500000 0 50001 Add Spectrum lt gt Del Spectrum Property of Light source 1 Yavelenth nm NumberOf Photons SourceEnergy N Add Light Source 10000 1 000000e 000 Apply Del Light Source Cancel Figure 8 1 Input dialog box for light source parameter The lower list shows the information of the light source which is chosen in the upper list including the 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 the 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 mc triangle mesh The upper list mentioned above is divided into two lists Figure 8 2 The Analytic 10 Light Source list shows the light sources which are analytic shape while the Mesh Light Source list shows the light sources which are mesh shape 3D Mesh Simulation Tissue Parameter Light Source Parameter CCH Parameter MC Simulation Parameter
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