Appendix A. What is MOSE?
Contents
1. Zoomt z Zoom Z Restore Restore Dsiplay Color or Gray C 2D amp 3D e Gray Pseudo 2D Image Number Image fo I I i Light Source CenterX c fo CenterY E fo CenterZ 4 fo NIE ruta C RE fo Figure 3 2 Main Window of 3D MOSE In the main interface of 2D 3D MOSE there are six menus named File Input Output Run Windows and Help respectively File has the functions such as open save save as new close print etc Input input parameters of the simulation Output output the results of the simulation such as absorption data transmittance data and data of CCD detectors Run after set the parameter of the program chose the submenu of Run the simulation of 2D 3D MOSE will be started Windows the operations of the opened windows Help online help window E 3 the switch button of the main interface between 2D MOSE and 3D MOSE T the pseudocolor transformation switch button 9 the switch button to stop or restart the photon trace of MOSE Step 2 Parameter Input 1 In the main window under the input menu select click Input Parameters First select single or multiple spectrum Select spectrum Spectrum t Single Spectrum Multiple Spectrum Cancel Figure 4 Select Spectrum 2 The Input Parameters window appears See Figure 5 There are four different input interface named Mouse2. MI Source NI Figure 9 3 Input Dialogue for the Parameter of Solid Light Source When the button Point Source 1s chosen the light source is a point one and the input interface 1s shown as figure 9 4 The parameters of the point source are smaller than those of the solid source There are only five parameters x y z SourceEnergy and NumofPhotons whose meaning are the same as the solid source X xcoordinates of the center position of light source See Figure 9 1 Y y coordinates of the center position of light source See Figure 9 1 Z z coordinates of the center position of light source See Figure 9 1 NumofPhotons the number of the photon packets to be traced See Figure 9 3 SourceEnergy the energy of the light source See Figure 9 3 Input 2D Monte Carlo Parameter Dialog Write Mouse Property Source CCD Detector I T Z SourceEnergy NumofPhotons Read 1 0 0 1 PointSource 1000000 Del Col Add Col Del Row Add Row C Normal Source Point Source MI Source Come Input Dialogue for the Parameter of Point Light Source Figure 9 4 When the button MI Source is chosen the parameters of the light source are inputted through the dialog shown as figure 9 5 while the shape is defined by the operator In 3D environment a basic shape of the light source is given and the modification to it can be realized by the operator MI stands for Manually Input Input 2D Nonte Carl
3. Property Source and CCD Detector respectively Given all the parameters the 2D 3D MOSE can run and simulate the propagation of photon packets Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Parameter Z Seperationt cm Muscle 0 0 0 01 Left Lungl 0 0 0 0 Left Lung 0 0 0 0 Left Lung3 0 0 0 0 Right Lungl 0 0 0 0 Right Lung 0 0 0 0 Right Lung3 0 0 0 0 Heart 0 0 0 0 Spinel 0 0 0 0 Spine 0 0 0 0 lt Figure 5 1 Input Parameters Dialogue in 2D MOSE 3 Enter the geometric parameters of the tissue in the mouse Mouse Input Interface Now let us see the explain how to input the parameters The tissue name is shown in the left of the input window Pull the Horizontal Scroll Bar at the bottom of the list to the right we will see other input parameters Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Shape Alpha degree Belta deer Muscle Polygon 0 0 0 0 Left Lungl Ellipse 0 0 0 0 Left Lung Ellipse 0 0 0 0 Left Lung3 Ellipse 0 0 0 0 Right Lungl Ellipse 0 0 0 0 Right Lung Ellipse 0 0 0 0 Right Lung3 Ellipse 0 0 0 0 Heart Ellipse 0 0 0 0 Spinel Ellipse 0 0 0 0 Spine Ellipse 0 0 0 0 OK Cancel Figure 5 2 Input Parameters Dialogue in 2D MOSE X x coordinates of the center location of the tissue See Figure 5 1 Y y coordinates of the center locatio
4. Cc 2D Image Number Image Ji I Light Source Centerx CenterY oOo CenterZ t i n e alpha Shape Distribution Number of photons SourceEnergy L1 L1 CCD Camera Ready Figure 12 15 1 Prepare to Modify the Shape of the Bezier Surface NOSE Nonte Carlo Optical Simulation Environment 3D Mouse Phantom WE File Input Output Run Reconstruction Window Help Ds e e efi a ale fel Assistant Rotate Axis Coordinate Axis X ERAS O Axis Y Lightin BAGA O Axis Z Zoomt Z Zoom Z Restore Dsiplay Color or Gray t 2D Image Number Image a Light Source CenterX CenterY CenterZ pe ni ef Shape Distribution Number of photons SourceEnergy m LI CCD Camera Ready Figure 12 15 2 The Shape of the Bezier Surface is modified NOSE Nonte Carlo Optical Simulation Environment Nodify the selected areal Aa File Input Output Run Reconstruction Window Help olsa ema ell Eel 2 Assistant Rotate Axis a Coordinate Axis X O Lighting O foda Y O Axis Z Zoom Z Zoom Z Restore Dsiplay Color or Gray 2D Image Number Image i Light Source CenterX CenterY 4 CenterZ i Distribution Number of photons SourceEnergy o m CCD Camera Ready Figure 12 15 3 The Modification of the Bezier Surface is finished Step 3 Simulation In the main window
5. Left Lung 230 0 3 5 Right Lungl 230 0 3 5 Right Lung Right Lung3 230 0 3 5 1 1 Left Lung3 1 230 0 3 5 1 1 1 230 0 3 5 Heart 1 37 160 0 2 0 Spinel 200 0 0 02 cnet Figure 8 Input Dialogue for the Optical Property of the Tissue 5 Input the geometric parameters of Light Source Source Input Interface The Source Input Interface offers the convenience to input the parameters of the light source The operator can choose a point source or a normal solid source with the Radio Buttons Source Type at the right bottom of the dialogue When the button Normal Source is chosen by default the light source is a solid one and the input interface 1s shown as figure 9 1 Input 2D Monte Carlo Parameter Dialog Mouse Property Source CCD Detector Write Parameter H T Z Alpha degree Belta degree Regn 0 0 LightSource 05 port Del Col Add Col Del How Add How Normal Source C Point Source C MI Source Figure 9 1 Input Dialogue for the Parameter of Solid Light Source The parameters are introduced one by one as follows X x coordinates of the center position of light source See Figure 9 1 Y y coordinates of the center position of light source See Figure 9 1 Z z coordinates of the center position of light source See Figure 9 1 Alpha Belta Gamma the rotated angle of the light source the definitions are the same as Mouse Input Interface Input
6. Property Source CCD Detector Write Shape a mm b mm c mm D LightSource Ellipsoid 2 0 2 0 2 0 Del Col Add Col Del Row Add Row Source Type Normal Source C Point Source MI Source Cancel Figure 9 7 Basic Shape Input of 3D MI Light Source 6 Input the parameter of CCD Camera Detector Input Interface It is better to assume that the detector 1s in close contact with the surface of the mouse phantom Therefore it collects all the photos into the detector surface As a result we d better design the CCD Camera through the parameters right out of the mouse phantom Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Write Parameter ajr z Alpha degree Belta degree Gamma 0 0 Read CCD Detector 0 O 0 Del Col Add Col Del Row Add Row Source Type C Normal Source C Point Source MI Source Cancel Figure 10 1 Input Dialogue for the Parameter of CCD Camera The parameters are introduced one by one as follows X x coordinates of the center position of CCD detectors See Figure 10 1 Y y coordinates of the center position of CCD detectors See Figure 10 1 Z z coordinates of the center position of CCD detectors See Figure 10 1 Alpha Belta Gamma the rotated angle of the CCD detectors the definitions are the same as Mouse Input Interface Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Param
7. 1 3D CCD Output of VBE in MOSE After running of the program the MOSE has recorded the raw data of absorption matrix transmittance matrix running time etc in the Program3DOutput txt file Values on the vertices are written in the 3DVertexFluxOutput txt file Data on four CCD sensor planes are recorded in CCD1_3D txt CCD2_3D txt CCD3_3D txt CCD4_3D txt Real MOSE Moreover we can find them in the same folder where the application software lies See Figure 25 3 i NOSEI 1 MT MGE FE TAT 585 a Qa d Pe bat E Het CD le C AMOSEL 1 E 85 Norton antivirus E EE Gid mrs pe se Bae o S0Mouse_Light xls eA PES c9 AeA Q BETTE p RETER HERE cgp IBM PRELOAD C E mnes C3 mnes q sinon PLES Microsoft Excel Hill 18 KE 3DMouse MI xls SH Microsoft Excel 19 KB 3DMouse Point Mu H Microsoft Excel 26 KB Mouse MI xls FH Microsoft Excel 22 KB MOSE1 1 rar WinRAR ER B IRSE CCDS 3D txt T 20 116 KB DVertexFlux utp HG Hd Qaa LA 3DMouse Light Mu Microsoft Excel 15 KB S0Mouse_MI_Multi Microsoft Excel 20 KB Mouse Light xls Microsoft Excel 21 KB Mouse MI Multi xls H Microsoft Excel bi 23 EB HOSE exe HHAH MonteCarlo MFC A CCD1 3D txt FEX 16 KB CCD4 3D txt FEX 79 116 KB 3DMouse Light zi Microsoft Excel HI 17 EB i 3DMo
8. 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Write a cm b em c om NumofPhoto 0 Ellipse 10000 Parameter Read LightSource Del Col Add Col Del Row Add Row Normal Source C Point Source C MI Source Cancel Input Dialogue for the Parameter of Solid Light Source Figure 9 2 Shape the geometric shape of the light source See Figure 9 2 In the Shape menu MOSE provides three kinds of distribution model Ellipse Polygon and Circle 2D MOSE and Ellipsoid Polyhedron Cylinder 3D MOSE Notice Among all the tissue shape there must be only one Polygon Polyhedron a semi axes along the x coordinates See Figure 9 2 b semi axes along the y coordinates See Figure 9 2 c semi axes along the z coordinates See Figure 9 2 Distribution the distribution of the light source in certain geometric area volume in the tissues See Figure 9 2 There are several choices for the distribution such as Uniform and Normal NumofPhotons the number of the photon packets to be traced in MOSE See Figure 9 3 SourceEnergy the total energy of the photon packets emitted from the light source See Figure 9 3 Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Write Parameter c em Shape NumofPhotons SourceEnergy Read LightSource 0 Ellipse 1000000 Del Col Add Col Del Row Add Row Source Type Normal Source C Point Source
9. Help onal eea eala fir Pr 2 2D House Phantom Figure 12 7 2 Delete an Anchor Point Click ka then use the left button to select an anchor point to be moved after that click the right button to set the new position of it The curve passes through the moved point will be updated automatically See Figure 12 8 1 and 12 8 2 NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help Das Hea eaa pla 2a 2D House Phantom Figure 12 8 1 Move an Anchor Point NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help aL ERES Ol S ra IK J I gt P a TA E E 1 Figure 12 8 2 Move an Anchor Point Click P then use the left button to select two sequential anchor points a new anchor point will be added between them after that click the right button to set the position of the new point A new curve connects the two selected anchor points and the new one will be generated automatically See Figure 12 9 1 12 9 2 and 12 9 3 NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help osa ea Ir T 3 r 2D House Phantom Figure 12 9 1 Add an Anchor Point NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help Dag S FIT axli e 2D House Phantom Figure 12 9 2 Add an Anchor Point HOSE Honte Carlo Optical Simulation Environment File Input Outpu
10. Carlo simulation application software We will find five files here MOSE exe is the application program Mouse xIs and 3DMouse xls are used for the parameter input in 2D and 3D respectively Files with Multi are for multiple spectrum while others without it are for single spectrum amp NOSE 1 MAE AG Bev EO IA MM Qa O 3 Da Ewx pu Hist CD ec MOSE1 1 v PED Norton AntiVirus Pee ii E Gm Sus Do SMA PBA HAME D Souss Light Mu sents Light si zd Microsoft Excel EH d crosoft Excel 18 KB mi TKE LPM PRES al rece Hil 15 KB m mazo r py Barer 3DMouse NI xls a H 1cr ft Excel D Sm H 19 KB BITTE Web a UI BE BEER SEE E j rb Point Mu mak H oft Excel rl Miers x MET TILA tags MI Multi SHE _Point xls xce f Mis crosoft Excel 24 KB uous aues as ims Light Mult dl Microsoft Mic crosoft Excel 28 KB 21 KB HL 24 KB Boney Jos 1 E Mouse Au ulti xls s Mouse Point xls H Mi crosoft Excel j E t KE H Microsoft Excel 23 KB KATAS Mo akda MM MFC A O Here q sem amp g ALNE E31 Bd Bg Bd cgp IBM PRELOAD C a Na MOSE exe Wink X wee 25 fi ae Figure 1 Unzip the MOSE rar file a HOSEL 1 ME BE EW CA CA TAW Bb a S O er 3 pes pare up EAE NTERUETEX ES mj m x XT By Haha att x el Am hk Fl Mouse Light xls Microsoft Excel 3DMouse MI xls pal 1 SUMouse Li
11. MOSE Molecular Optical Simulation Environment Software for Photon Tracing in Biological Tissues Ge Wang Ph D Jie Tian Ph D Bioluminescence Tomography Laboratory Virginia Tech Wake Forest University V A U S A Medial Image Processing Group Institute of Automation CAS Beijing P R C User s Manual Release 1 1 Beta Supported by NIH NIBB 1R21EB001685 01 Copyright BLT Lab Virginia Tech Wake Forest University V A U S A MIPG Institute of Automation CAS P R C Appendix A What is MOSE 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 MOSE works 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 greater depth in the following sections 1 Input the 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 Output These three files are bmp files and also you can find the raw data in programoutput txt and CCD txt In MOSE we us
12. TissueListh mcUniform h MonteCarlo h MonteCarloDoc h MonteCarloview h Resource h StdAfxh TraceDig h amp Compound List m Class Hierarchy E Compound Members Figure 17 HelplContent Appendix D Virtual Biological Environment VBE in MOSE Step 1 Start 1 It is easy to obtain the main interface of VBE in MOSE through the switch button in the toolbar NOSE Monte Carlo Optical Simula ion Environment l ox File Input Output Run Reconstruction Wa idew Help ty 3D Raw Data Interface Select spectrum Spectrum C Single Spectrum Multiple Spectrum Cancel Figure 18 1 Main Window of VBE in MOSE In the main interface of VBE in MOSE there are six menus named File Input Output Run Windows and Help respectively File has the functions such as open save save as new close print etc Input input parameters of the simulation Output output the results of the simulation such as absorption data transmittance data and data of CCD detectors Run after set the parameter of the program chose the submenu of Run the simulation will be started Windows the operations of the opened windows Help online help window 23 the switch button of the main interface between 2D MOSE and 3D MOSE the pseudocolor transformation switch button 9 the switch button to stop or restart the photon trace of MOSE uls the button to restart or stop the VBE i
13. combo box then the original mesh number of that model will be shown in the gray edit box Secondly modify the number in the white edit box which is the target mesh number for the simplification Press OK button to start the simplification process which takes a few seconds The simplified model will replace the original one to be shown in the left of the right window The simplification process can be repeated to meet the requirement of operator When finished click button P Figure 22 3 Mesh Simplification Dialog in MOSE Step 7 Geometric Similarity Metric The geometric similarity metric GSM can represent the similarity of models the smaller the GSM value the fewer the differences between models More information is available in the Technical Report of MOSE 1 Click the button 9 the Geometric Similarity Metric Dialog appears See Figure 23 1 Geometry Similarity Metric cs K Choose A Mesh o Facets Number Original 256032 Facets Number Now 8824 GSM V to V 0 207528 GSM Combine 0 0483706 Figure 23 1 Geometric Similarity Metric Dialog in MOSE First choose a model in the combo box then the original number of mesh and that after simplification will be shown in the corresponding edit box And then press the button Show the GSM value calculated in two methods will be shown in the third and forth edit box Step 8 Changes to the Light Source and CCD Detector The operation to modify the local shape of t
14. construction Click the button o the Set Threshold Dialog appears See Figure 20 1 MOSE can segment the volume data and extract the tissue s with the grayscale at the given threshold then reconstruct the surface model of these tissue s The model is shown in the right of the main window See Figure 20 2 Set Threshold High Threshold 0 Low Threshold 0 Cancel Figure 20 1 Set Threshold Dialog in MOSE Figure 20 2 Surface Models reconstructed from the volume data Step 4 Optical Parameter Input 1 After the surface model of one tissue has been reconstructed click the button then the dialog shown as Figure 21 1 or 21 2 appears which provides a way to specify the optical property of that tissue Press OK button when finished MOSE will add the tissue to the VBE In the case of multiple spectrum three groups of absorption coefficient and scattering coefficient need to be input which correspond to three wave bands Optical Property Tissue muscle Optical Property Refractive Index 1 37 Anisotropy Coefficient 0 9 Absorption Coefficient 0 01 1 mm Scattering Coefficient 4 1 mm Cancel Tissue Optical Property Refractive Index Anisotropy Coefficient Absorption Coefficient Short RE 1 mm Scattering Coefficient Short RE Timm Absorption Coefficient Middle 0 1 mm scattering Coefficient Middle 0 Timm Absorption Coefficient Long O 1mm scattering Coefficient Long O Timm Cancel Figur
15. e 21 2 Set Optical Property Dialog for Multiple Spectrum in MOSE Step 5 Add Models to VBE 1 By taking Step 4 and Step 5 repeatedly the tissues of interest can be added to the VBE For preventing misoperation the button 4 is provided to clear all the tissues have been added A typical VBE includes the models of the skin the muscle and the organs of interest And the typical adding order is from outer models to the inner For example that is the skin the muscle and the organs 2 When all the tissues have been added click the button l then the surface models of these tissues will be shown together as that in the real animal body in translucent mode See Figure 22 1 the muscle together with the top bottom section of the skin are hidden for better view Figure 22 1 Surface Models of a Mouse Thorax Skin Muscle and Lung in MOSE These models can respond to several mouse actions left button dragging leads to the rotation of the model right button dragging can move the model within the window and wheel rolling will do the zoom All these operations provide a user friendly view of the models both in general and in detail Step 6 Model Simplification Click the button 4 the Model Simplification Dialog appears See Figure 22 2 Cf Simplification Choose a model muscle Original Mesh Number 256032 Target Mesh Number 1 0000 Cancel Figure 22 2 Mesh Simplification Dialog in MOSE First choose a model in the
16. e centimeter cm in 2D or millimeter mm in 3D or VBE virtual biological environment as the basic units of length How do I input the parameters MOSE has a very friendly user interface And it offers an efficient approach for us to input the parameters If we unintentionally make mistakes while inputting the parameters we simply correct them from the area where we have input just now We can add more kinds of tissues if we need This is especially useful when the kinds of tissues are more than the default settings How does 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 photons absorption 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 transmission information Through these records MOSE can give the absorption and flee map of the photons Can I run MOSE on my computer Until now MOSE can run on Microsoft Windows 98 2000 NT XP Appendix B Getting started with MOSE Step 1 Run MOSE Im Click the MOSE rar file and unzip the file into the mc folder Double click the folder we will find five files The first and easy way is to double click MOSE exe file It immediately starts the Monte
17. econstruction Window Help Diem e c eg sa sa 2 Assistant 7 Coordinate O Lighting Zoom Z Zoom Restore Color or Gray 3 Gray Pseudo P n o e o alpha o Shape Distribution Number of photons o SourceEnergy fa Enable O Modify CCD Camera Figure 15 5 2D CCD Output of 3D MOSE r HOSE1 1 THE MEL FEU KAW Tam Ehh Qa 90 E Pake O RAR sik BEA es oes ewes H QSR ie Jmm x M 3DMouze Light xls 3DMaouse Light Mu 3DMeuze Light si KANILA E H Microsoft Excel PA Microsoft Excel 4A Microsoft Excel 18 KB Cl 18 KB coll 17 KB C3 eT z i amp Tac T PIE m s lt 3IMouse MI xls gt 3DMouze MI Multi 3IMouse Point xls Web pH Microsoft Excel HA Microsoft Excel HA Microsoft Excel kd Exp EXE 13 EB cH 20 EB cul 4 KE 3DMeuze Point Mu Mouse_Light xls Mouse Light Mult EH Microsoft Excel ES Microsoft Excel Microsoft Excel zB EB m P1 KB HUL 24 KB c IEM_PRELOAD C7 Mouse MI xls gt Mouse MI Multi xls 1 Mouse Foint x1s O KATAS HJ Microsoft Excel AA Microsoft Excel HA Microsoft Excel ET OU 22 KB CH 23 KB rik 71 KB p 226 Pc Fe hi MOSEL 1 rar ewe MOSE exe WinRAR REST ky a VHF amp 3 FIL ESPRS 1 061 EB mox MonteCarlo MFC A Figure 16 Output files of MOSE Programoutput txt and CCD txt After
18. enterZ a ra I b 4 c E 1 o n e alpha Shape Distribution Number of photons SourceEnergy m m CCD Camera Click to finish the VOI selection Figure 12 13 Confirm the ROI Selection of 3D MOSE me HOSE onte Carlo Optical Simulation Environment kf AI Jp a UBI F A File Input Output Run Reconstruction Window Help naa off aul elel eal Assistant Rotate Axis Coordinate Axis X iahti O Axis Y O Lightin bi ies O Axis Z Dsiplay Color or Gray KS 2D Image Number Image 1 I Light Source Center X2 m CenterY CenterZ a b 1 o c H n e alpha Shape x Distribution Number of photons SourceEnergy LI Oo CCD Camera Ready Figure 12 14 The ROI Selection of 3D MOSE is confirmed Finally use the S button to modify the shape of the Bezier surface on the ROI which replaces the original surface on the ROI of the light source Click the button to turn the control point of the Bezier surface to be visible By dragging the control point the operator can modify the shape of Bezier surface See Figure 12 15 1 to 12 15 3 NOSE Nonte Carlo Optical Simulation Environment 3D Mouse Phantom a File Input Output Run Reconstruction Window Help Dau ea e a reel 2 Assistant Rotate Axis A Coordinate Axis X ba O Axis Y O Lightin ra Te O Axis Z Zoom Z Zoom Z Restore Dsiplay Color or Gray tg ic gt
19. eter Shape a cm gt cm E cm HumofDetect 12 0 CCD Detector Circle 1 8 Write Read Del Col Add Col Del Row Add Row Source Type Normal Source C Point Source MI Source Figure 10 2 Input Dialogue for the Parameter of CCD Camera Shape the geometric shape of the CCD detectors See Figure 10 2 In the Shape menu MOSE provides three kinds of distribution model Ellipse Polygon and Circle 2D MOSE and Ellipsoid Polyhedron Cylinder 3D MOSF a semi axes along the x coordinates See Figure 10 2 b semi axes along the y coordinates See Figure 10 2 c semi axes along the z coordinates See Figure 10 2 NumofDetectors the number of the CCD detectors See Figure 10 2 Now we have finished inputting the whole parameters of MOSE If we want to save them as the default settings please press Write up right corner to save them After press Write a dialog will come out to tell us if the data has been written successfully See Figure 11 Montecarlo Xx Successful write to database Figure 11 A Dialog indicating that data has been written successfully Now press OK button we will see an image appears in the main window which is made up of the tissues set by the Input Parameters Dialogues Figure 12 1 2D MOSE Figure 12 2 3D MOSE Then we can launch the simulation process at any moment NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Hel
20. ght Mu NABA Excel E 3DMeuse MI Multi T 3DMouze Light zi J Microsoft Excel Et 1T EB 3DMouse Point xls Microsoft Excel H Microsoft Excel 13 EF 20 KB E 1 Mouse Light xls T Ee Excel Mouse MI Multi xls 1585 Microsoft Excel 23 KB MOSE exe fi FA te Ae Montecarlo MEC A Microsoft Excel e4 EB p Sale Tae QM TRS Web Y i 3DMouse Point Mu o Microsoft Excel eb EB x Merti fa 1 Mouse MI xls Microsoft Excel Mouse Light Mult Microsoft Excel P4 KB Mouse Point xls Microsoft Excel HERE ago IBM PRELOAD C tana Qo KEN q unm FLEE MOSE1 1 rar WinRAR fe fart 1 061 KB Figure 2 The unzipped folder 2 Double click the MOSE exe file application software immediately NOSE Nonte Carlo Optical Simulation Environment it will start Monte Carlo simulation File Input Output Run Window Help Dau S alela 63 2 2D House Phantom Main Window of 2D MOSE Figure 3 1 The main interface of 2D MOSE ss the default interface shown as Figure 3 1 Also it 1s easy to obtain the main interface of 3D MOSE through the switch button 23 in the toolbar NOSE Nonte Carlo Optical Sim tation Environment File Input Output Run Reconstructi Window Help 2e 3D Monte Carlo Simulation Assistant Rotate Axis d Coordinate Axis X tahti O Axis Y Lightin B t O Axis Z
21. he light source 1s the same with that in the 3D MOSE Changes of some parameters can be done through the control panel See Figure 24 2 Generally four detector sensor planes and corresponding parallel lenses are perpendicular to xOy plane as shown in Figure 24 1 Detectors surround the phantom with an increasing degree of 90 Parameters of the first detector and lens can be set in the control panel the button to hide or show CCD sensor planes or lenses Default is to hide them Figure 24 1 Detectors and Lenses Step 9 Simulation in VBE The operation is the same with that in the 2D 3D MOSE L LightSource Shape Ellipsoid Distribution Uniform Number of photons 100000 SourceEnergy 1 CCD Detector Centex CenterY CenterZ a a E Shape Rectangle Normal X Seperation Z Normal Y mx Seperation A Normal Y O Enable Modify 20 20 35 ns 20 Figure 24 2 Simulation Window of VBE in MOSE Step 9 Output of VBE in MOSE The CCD Output gives the photons which have fled away from the mouse tissue and detected by the CCD Camera See Figure 25 1 VBE in MOSE with 400 000 photons for example The default is not to show the colors on CCD sensor planes If you want to see the CCD click button Ko and mostly shrink the whole image Figure 25
22. ical Simulation Environment File Input Output Run Window Help osal eea leaa o x b P 2a 2D Nouse Phantom Figure 12 4 Define the Anchor Point for MI Light Source in 2D Based on every three sequential anchor points one section of the light source boundary is defined A curve is generated to connect these anchor points See Figure 12 5 NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help oea ees 9 2 85 m 0 x r P al 2a 2D Nouse Phantom BE Figure 12 5 The Curve Connects the Anchor Points If the definition of the light source boundary is finished click the right button to set a finishing point which will be connected to the first anchor point See Figure 12 6 NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help l osal ela olea E xele 2 2e 2D House Phantom Figure 12 6 Finish the Definition of Light Source Several methods are also provided to modify a defined light source Click x then use the left button to delete an anchor point The anchor points before and after the deleted one will be connected automatically See Figure 12 7 1 and 12 7 2 NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help osal S olaaa E xele 2e 2D House Phantom Figure 12 7 1 Delete an Anchor Point a NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window
23. l Left Lung Left Lung3 Right Lungl Right Lung Right Lung3 Sternum Y 0 65 1 1 1 05 0 0 0 65 1 1 0 65 0 65 0 0 1 05 R 0 0 0 0 0 0 o o oa o ao oao a a a 0 0 ionk cm 0 0 0 0 0 0 0 0 0 0 Read Del Col Add Col Del Row Add Row Source Type C Normal Source C Point Source C MI Source Delete a Row ionk cm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Read Del Col Add Col Add Row Source Type C Normal Source C Point Source C MI Source Figure 7 2 Input Dialogue After Deleting a Row Notice Since each tissue has its own corresponding properties when we deal with want to Delete or Add some tissue we must Delete or Add the corresponding properties in the Property menu or MOSE will mention us that there 1s something wrong with our action 4 Input the optical parameters of each tissue Tissue Input Interface With the tissue input interface the operator can easily input the optical properties of each biological tissues such as refractive index scattering index absorption index and anisotropy index respectively The functions of the buttons located at the right of the dialogue are the same as the Mouse Input Interface Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Parameter Refractive Scattering 1 cm Absorption Muscle 1 37 40 0 0 1 Left Lungl 230 0 3 5
24. n 3D MOSE Click the button S to decide whether the mouse model is drawn See Figure 12 13 1 and 12 13 2 9 NOSE i ical s i E3 Lam File Input Output Run Reconstruction Window Help EN X ojal ela elema alel Ee 3 Assistant Rotate Axis Coordinate Axis X ighti O Axis Y CO Lightin ha TUM O Axis Z Dsiplay Color or Gray 2D Image Number Image I Light Source CenterX CenterY CenterZ a b c n e alpha Shape Distribution Number of photons SourceEnergy m m CCD Camera Ready Hi Figure 12 13 1 Enable Mouse Shown in 3D MOSE E 3 HOSE Nonte Carlo Optical Sim ca File Input Output Run Reconstruction Window Help o x Da bd 22 58 nia e p g e Assistant Rotate Axis 4 Coordinate Axis X O Lighting O Axis Y O Axis Z Zoom Z Zoom Z Restore Dsiplay Color or Gray 2D Image Number Image i i Light Source CenterX CenterY 4 CenterZ z ac pe b C t n e alpha Shape Distribution Number of photons SourceEnergy L1 L1 CCD Camera Ready NUM Figure 12 13 1 Disable Mouse Shown in 3D MOSE A typical light source modification process includes several steps as follows First click El then use left button to select a plane the intersection region of that plane and the light source forms the ROI The selection operation has several steps pressing d
25. n MOSE Step 2 Volume Data Input 1 In the main window under the file menu select submenu Load Volume Data click Load Raw File After raw file is selected the Open Raw File Dialog appears See Figure 19 1 Given all the information listed in the dialog the MOSE can load the raw data to reconstruct the VBE Open KAF file Filename D Mouse Data ehresult raw ones Information Width 512 Pixel interval 0 0781 mm Height 512 Pixel interval 0 0781 mm Number of slicel49 Slice interval 93 mm Number of channels DEM Data type unsigned char 8 bits Head length Na SeparationAngle go Separation rZ EN mm Cancel Figure 19 1 Open Raw File Dialog in MOSE 2 Click the OK button we will see three images appear in the left of main window which are the views of CT slices from three directions See Figure 19 2 Surface information Set threshold NOSE Nonte Carlo Optical Simulation Environment 3D P use Phantom A File Input Output Run Reconstruction Window elp Dial eels c elf kada ho ajaja ze o t Figure 19 2 Three direction views of CT slice in MOSE In the toolbar of VBE in MOSE there are seven new buttons shown as follows B the button to view the CT volume data information n the button to view the surface model information 1f reconstructed M P these buttons provide a browse of CT slices ol the button to start the reconstruction of surface model Step 3 Surface Model Re
26. n of the tissue See Figure 5 1 Z z coordinates of the center location of the tissue See Figure 5 1 SeperationX the separation of x coordinate See Figure 5 1 SeperationY the separation of y coordinate See Figure 5 1 SeperationZ the separation of z coordinate See Figure 5 1 Shape the geometric shape of the tissue See Figure 5 2 In the Shape menu MOSE provides three kinds of distribution model Ellipse Polygon and Circle 2D MOSE and Ellipsoid Polyhedron Cylinder 3D MOSE Alpha Belta Gamma the rotated angle of the tissue e g Figure 4 3 1s the schematic of rotated angle in the case of two dimensions Figure 5 3 schematic of rotated angle in the case of two dimensions Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Gamma degree a cm b em c em Muscle 0 0 1 8 1 8 0 0 Left Lungl 0 0 0 4 0 4 0 0 Left Lung 0 0 0 45 1 25 0 0 Left Lung3 0 0 0 4 0 4 0 0 Right Lungl 0 0 0 4 0 4 0 0 Right Lung 0 0 0 0 Right Lung3 0 0 h 0 0 Heart 0 0 0 0 Spinel 0 0 1 0 0 Spine2 0 0 0 0 cnet Figure 5 4 Input Parameters Dialogue in 2D MOSE a semi axes along the x coordinates See Figure 5 4 b semi axes along the y coordinates See Figure 5 4 c semi axes along the z coordinates See Figure 5 4 Add a new tissue Press the button Add Row right bottom of the input window an input dialogue will be shown as Figure 6 1 The operator can in
27. o Parameter Dialog Mouse Property Source CCD Detector Write Parameter a Y Iz Alpha degree Belta degree s m 0 0 BISource DD NO Del Col Add Col Del Row Add Row Source Type C Normal Source C Point Source Cancel Input Dialogue for the Parameter of MI Light Source Figure 9 5 The parameters are introduced one by one as follows X xcoordinates of the center position of light source See Figure 9 5 Y y coordinates of the center position of light source See Figure 9 5 Z z coordinates of the center position of light source See Figure 9 5 Alpha Belta Gamma the rotated angle of the light source the definitions are the same as Mouse Input Interface Distribution the distribution of the light source in certain geometric area volume in the tissues See Figure 9 6 There are several choices for the distribution such as Uniform and Normal NumofPhotons the number of the photon packets to be traced in MOSE See Figure 9 6 SourceEnergy source See Figure 9 6 the total energy of the photon packets emitted from the light Input 2D Nonte Carlo Parameter Dialog Write Mouse Property Source CCD Detector Parameter Distribution NumofPhotons SourceEnergy f Read BISource Uni form 1000000 Del Col Add Col Del Row Add Row Normal Source C Point Source Figure 9 6 Input Dialogue for the Parameter of MI Light Source Input 3D Monte Carlo Parameter Dialog Mouse
28. own the left button dragging the mouse to another position and releasing the button A plane will be defined by the position where the button is pressed and that 1s released See Figure 12 12 NOSE Nonte Carlo Optical Simulation Environment 3D Mouse Phantom 5 File Input Output Run Reconstruction Window Help Dea eea olla a e e 5 fag s Assistant Rotate Axis Axis X O Axis Y O Axis Z Zoomt Z Zoom Z Restore Dsiplay Color or Gray Co EF 6G Coordinate O Lighting 2D Image Number Image L Light Source CenterX tO Distribution Number of photons SourceEnergy LI LI CCD Camera Ready Figure 12 12 ROI Selection of 3D MOSE Secondly if the plane defined by ROI selection operation does intersect with the light source the button E will turn to be available See Figure 12 13 Click it to confirm the ROI selection then a Bezier surface will be generated and shown in yellow See Figure 12 14 deg CI r r c P 211 D f t Ju monte Lario Upti Cal PIAIMULACULON Environment LID Bouse uictum d x ES a A File Input Output Run Reconstruction Window Help osal 5 e 5 o sf amp en en Assistant Rotate Axis Coordinate Axis X iahti O Axis Y O Lightin a ides O Axis Z Zoom Z Zoom Z Resto re Dsiplay Color or Gray 2D Image Number Image I 1 Light Source CenterX CenterY C
29. p Deal e S zz Figure 12 1 Image of 2D Mouse Phantom and CCD Camera a NOSE Nonte Carlo Optical Simulation Environment fe File Input Output Run Reconstruction Window Help i S clef Ba oeeie tl E 3D Mouse Phantom Assistant Rotate Axis Coordinate Axis X ighti O Axis Y Lightin iiie O Axis Z Zoom Z Zoom z Restore Dsiplay Color or Gray e 2D 3D e Gray Pseudo 2D Image Number Image poo n o e fa alpha o Shape Distribution Figure 12 2 Image of 3D Mouse Phantom and CCD Camera 7 Operations for Manually Input MI Source In 2D MOSE If the MI Source 1s chosen in the source input step the interface of 2D MOSE will be somewhat different NOSE Nonte Carlo Optical Simulation Environment my File Input Output Run Window Help 7 If Re ady EE EN om 4 Figure 12 3 Image of 2D Mouse Phantom and CCD Camera for MI Light Source the button to enable the setting of the anchor points the button to delete an anchor point E the button to move an anchor point i the button to add an anchor point C the button to clear the manually input light source A typical light source setting includes several steps as follows First click then use left button to define the anchor points See Figure 12 4 NOSE Nonte Carlo Opt
30. p and Flee Map can be saved through the procedure introduced above as saving the mouse phantom NP Figure 15 2 Flee Map of 2D MOSE CCD Output It gives the photons which have fled away from the mouse tissue and detected by the CCD Camera See Figure 15 3 2D MOSE and Figure 15 4 3D MOSE with 10000 photons for example Figure 15 3 CCD Output of 2D MOSE NOSE Nonte Carlo Optical Simulation Environment 3D Photon Flee Map File Input Output Run Reconstruction Window Help osa S elea x aler ee 2 Assistant i 0 0000E 00 Coordinate O Lighting Zoom Z Zoom Z Restore Dsiplaysam Color or Gray C Gray Pseudo F Image Number 7 3409E 002 n fa e o alpha o Shape Distribution Number of photons o SourceEnergy o O Enable O Modify CCD Camera Figure 15 4 3D CCD Output of 3D MOSE Display display 2D 3D output interface 3D When the 3D option 1s chosen the 3D output image of CCD detectors can be seen as Figure 14 4 2D When the 2D option is chosen and the longitude value is given the 2D output image of the certain CCD detectors can be seen shown as Figure 15 5 Color or Gray chose the pseudo color Gray if chose the Gray option the display is used the gray color Color 1f chose the Color option the display 1s used the pseudo color NOSE Nonte Carlo Optical Simulation Environment 3D CCD Detector Map DM File Input Output Run R
31. photon by pressing the icon stop in the toolbar When total photon running has stopped we can see the output of MOSE NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help 0Sa x Ele olala ad ol 2D House Phantom 166 photon running 1 complete a Figure 14 1 Simulation Window of 2D MOSE NOSE Nonte Carlo Optical Simulation Environment 3D Mouse Phantom CA File Input Output Run Reconstruction Window Help Df gleja a aell 2 Assistant Rotate Axis Coordinate Axis X O Axis Y O Axis Z Zoom Z Zoom Z Restore Dsiplay Color or Gray O Lighting 2D Image Number Image e UUU Light Source CenterX CenterY 4 CenterZ n e alpha Shape Distribution Number of photons SourceEnergy LI L1 CCD Camera CenterX CenterY 95 photon running 9 complete BE ED E Figure 14 2 Simulation Window of 3D MOSE Step 4 Output of MOSE With pseudo color chosen the output of 2D MOSE includes several parts 2D Absorption Map Figure 15 1 2D Flee Map Figure 15 2 and the CCD Output Figure 15 3 2 2D Photon Absorption Map 10 X Figure 15 1 Absorption Map of 2D MOSE Absorption Map It gives the absorption map of photons absorbed in the mouse tissue See Figure 15 1 with 1000 photons for example Flee Map It shows the photon flee map See Figure 15 2 with 10000 photon Both Absorption Ma
32. put the name of the tissue which you want to add in the blank text Then click the OK button A new row will appear in the input window as Figure 6 2 indicates The parameters of the new tissue must be manually input into the blank list And clicking the Write button all the parameters of the new tissue will be saved to the data base Input the title of inserted row or column X O cw Figure 6 1 Input window for a New Tissue Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Parameter Left Lung3 Right Lungl Right Lung Right Lung3 Heart Spinel Spine2 Sternum New Tissue 0 65 0 65 I 1 05 0 0 0 0 0 0 0 0 1 45 0 0 1 45 0 65 SEI D 0 0 0 0 cCIcocjgcoj c c cGI oOJ oco 0 0 1 65 Cancel I Y Z Seperationt cm zb 0 oo So Le aS ea cor Ic Write Read Del Col Add Col Del Row Add Row Source Type v C Normal Source C Point Source C MI Source Figure 6 2 Adding a New Tissue Delete a row Choose the row we want to delete as Figure 7 1 indicates and press Button Del Row Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Parameter Left Lung2 Left Lung3 Right Lungl Right Lung Right Lung3 Y Z Seperat 0 0 0 0 0 0 Figure 7 1 Input 2D Nonte Carlo Parameter Dialog Mouse Property Source CCD Detector Parameter Left Lung
33. running of the program the MOSE has recorded the raw data of absorption matrix transmittance matrix running time etc in the Programoutput txt file 2D MOSE or Program3DOutput txt file 3D MOSF and the bioluminescent signals of the CCD detectors in CCD txt file 2D MOSE Moreover we can find them in the same folder where the application software lies See Figure 16 ProgramOutput txt Program3DOutput txt including the absorption data the transmittance data and the program running time CCD txt CCD 3D txt the bioluminescent signals of the CCD detectors Appendix C MOSE Help Tf you have any questions about the functions and classes used in MOSE you can refer to the Help File in MOSE by click HelplContent in the toolbar then you will see the help file like Figure 17 shows E Montecarlo E S x Gc o amp Hide Locate Back Forward Stop Refresh Home Print Options Meters fees Search SIN Main Page Class Hierarchy Alphabetical List Compound List File List E Compound Members za O File List AbsorbYiew h ChildFrm h em MonteCarlo Documentation Fleeview h Q amp InputDialog h Q amp MainFrm h l mcDetector h Generated on Fri Jul 18 14 28 32 2003 for MonteCarlo by doxygen 1 3 mcDistribution h mcEllipse h mcErrorh mcLightSource h mcMatrixh mcMouse h mcNormal h mcOpticalProperty h mcOutputh Ge mcPhoton h mcPolygon h mcShape h mcTissue h mc
34. shape of the light source they will be introduced latter Click the button rl then drag the light source to a suitable position The light source will response to the moving of mouse simultaneity See Figure 12 12 1 and 12 12 2 G2 dr 2 C Co DL Ww f O J vi onte Arlo Dpt cal mulati on ENnNVironment 3D ouse Fhantonm LP File Input Output Run Reconstruction Window Help oea Eels offs cepe Bm O Assistant Rotate Axis Coordinate Q Axis X E ES O Axis Y O Lightin re To O Axis Z Zoom Z Zoom Z Restore Dsiplay Color or Gray 2D Image Number Image L Light Source CenterX CenterY 4 CenterZ n e o alpha o Shape Distribution Number of photons SourceEnergy O L1 CCD Camera Ready Figure 12 12 1 The Moving of Light Source in 3D MOSE pre r f 1 P prz DI nf IO SE monte ario Uptical IBULATION Environment LIL ouse Phantom n File Input Output Run Reconstruction Window Help Djs jul e AJ aep eel 2l Assistant Rotate Axis Coordinate Axis X ERES O Axis Y O Lightin MTM O Axis Z Zoomt Z Zoom Z Restore Dsiplay Color or Gray 2D Image Number Image Light Source Centerx H CenterY CenterZ t n e m alpha o Shape Distribution Number of photons SourceEnergy m L1 CCD Camera Ready Figure 12 12 1 The Moving of Light Source i
35. t Run Yindow Help Das e 4 S 9 2 8 7a e x p r A 2 2D House Phantom Figure 12 9 3 Add an Anchor Point Click e the defined light source will be erased See Figure 12 10 NOSE Nonte Carlo Optical Simulation Environment File Input Output Run Window Help Das Gad ue amp x 2 Aa cl Clear all the HI source Figure 12 10 Clear the Light Source 8 Operations for Manually Input MI Source In 3D MOSE The interface of MI light source in 3D MOSE is shown in Figure 12 11 NOSE Nonte Carlo Optical Simulation Environment 3D Mouse Phantom Wy File Input Output Run Reconstruction TE Buttons for MI operations aja es pef ele fer a Assistant Rotate Axis Coordinate Q Axis X NURSE O Axis Y O Lightin DS O Axis Z Zoom Z Zoom Z Restore Dsiplay Color or Gray 2D Image Number Image Light Source CenterX CenterY Centerz a b c 4 n e alpha Shape E Distribution Number of photons SourceEnergy m Figure 12 11 Image of 3D Mouse Phantom and CCD Camera for MI Light Source ka the button to select the region of interest ROI la the button to confirm the selection of ROI the button to modify the Bezier surface the button to move the light source ka the button to enable disable the drawing of mouse model The first three buttons are used to modify the
36. under the Run menu select click Simulation a dialog will come out for you to select which kind of photon trace you wish to display on the screen See Fig 13 Photon Trace Option Trace Photon Trace None t Trace All C Trace Photons Reaching CCD Trace Photon From To OK Cancel Figure 13 Option Dialog Window for the Simulation Here Trace All means display all the photon traces on the screen Trace Photons Reaching CCD means display the photons which reached on the CCD Camera Trace Photon From To means that you can display the photons in the range you given Then Press OK to start the simulation the program can run with all the parameters chosen in Step 2 We can audit the whole procession of simulation through the information given in the simulation window shown as Figure 14 1 2D MOSF and Figure 14 2 3D MOSE In the window we can see the different traces of photon packets indicating with different colors Moreover a Process Bar located at the left bottom corner of the window indicates the process of the whole simulation when running 251 photon running indicates that the program has finished 251 photon packets tracing 25 complete indicates that about 25 of the total photon packets has been finished tracing The process bar shows a vivid expression of the simulation process The bend shows the photon trace of its whole life Notice We can stop tracing the
37. use Paoint xlsz 1 Microsoft Excel Hill 24 KB Mouse Light Mult Microsoft Excel 24 KB Mouse Foint xls Microsoft Excel 1 KB Mitk dll dll MARI CCI 3D txt MA 22 116 KB Frogram3ll nutput txt HANG 159 KB Figure 25 3 Output files of MOSE Programoutput txt and CCD _3D txt Appendix E Data formats available in Virtual Biological Environment VBE in MOSE Several formats for surface data after simplification are supported by MOSE including SPL OFF PLY and SMF while RAW and BMP are for volume data not for the simplified surface mesh data NOSE Nonte Carlo Optical Simulation Environment igo Input Output Run Reconstruction Window Help Hew CtrltN pen Ctrl 0 Close Save Ctr1t5 Save As Load Volume Data d Load RAW File Save Surface Model gt Load BMP File Load SPL File Load OFF File Load PLY File Load SMF File Print Setup
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