128055_Rev01 Quantum FX uCT User's Manual.book
Contents
1. Cross hair location in the X plane Cross hair loation in the Y plane Grayscale value at the crosshair location 40 Quantum FX uCT Software User s Manual Chapter 5 Viewing Images 5 4 3D Viewer Optional Plugin The 3D Viewer is an optional plugin that provides tools for rendering 3D reconstructions classifying the image data and visualization and viewing the 3D reconstruction from different perspectives The volume rendering controls provide a histogram based method for classifying the 3D reconstruction To open the 3D Viewer 1 Double click a thumbnail or series row in the Database window 2 Click the button in the Viewer that appears The Volume Rendering Control panel and 3D Viewer window appears Figure 5 4 Figure 5 4 Volume Rendering Control Panel and 3DViewer BI 3DViewer File F Language L Help H ID 1 Study 20121206 Series 145954 Volume Rendering Control Preset Rendering Selection Image Control Banal NG m etanat EH Component Selection Bone Lil Part 2 DJ UC EJ sl 93 o SEL 2 ms 3DCOLOR Table 5 5 Volume Rendering Controls Item Function Present Rendering Allows the use of custom color tables Selection Type select leg Comment Ni SDCOLOR D 3DCOLOR i Jie Quantum FX uCT Software User s Manual Chapter 5 Viewing Images Table 5 5 Volume Rendering Controls continued2. Item Function Component Selection Part select CUBES e E VT a O sa Tools for classifying the image data See page 43 for more details Image Control Click a blue arrow to rotate the 3D reconstruction 90 about the x y or z axis To freely rotate the 3D reconstruction about the x or y axis 1 Click the button 2 In the 3DViewer press and hold the mouse button while dragging the mouse ata fe EZ r3 eeHg E a E Click an arrow to rotate the 3D reconstruction about the z axis To freely rotate about the Z axis 1 Click the f arrow then click an image 2 Press and hold the mouse key while moving the mouse Translates the slice image in the windowpane Click the lt j button to return to the default view Scales the slice image Show or hide the x and y axis crosshairs Show or hide the perspective indicator in the 3D Viewer Opens the Tool Box with controls for setting shading parameters and the level of details in static and moving images in the optional 3D Viewer See Table 5 7 on page 47 for more details on the Tool Box Resets to the default slice view or the default display if the image has been rotated translated or scaled O ut Use these controls to cut the 3D reconstruction and remove voxels from the Hides all voxels above the y axis crosshair Y axis crosshair 42 Quantum FX uCT Software User s Manual C
3. eis HERES EEAS o DREI i B Ui ta m ix i o PX Gl KAB ma C3 Table 5 4 Viewer Functions Item Function Start Click to import other CT data vox into the Viewer Opens the Database window ie de d E Switches between images in the database Click U to open the next database image in the same instance of the Viewer Click Sond to open the previous database image in the same instance of the Viewer Al Opens the SimpleViewer Opens the optional 3D Viewer plugin EM Scrolls through slice images in a windowpane using the mouse wheel Quantum FX uCT Software User s Manual Chapter 5 Viewing Images Table 5 4 Viewer Functions continued Item Function 2x bx or 10x SHE o Translates the slice image in the windowpane Rotates the slice image within a plane Scales the slice image Magnifies a selected area of the slice image Right click to select a different magnification 2x bx or 10x Alternatively click the R button the to change magnification Area within the bounding box is magnified Magnified image area Changes the window and level settings to change the image display Use the keyboard up or down arrows Alternatively press and hold the mouse button while you drag the mouse up or down in a windowpane Reverses the gray scale color table Click the B butt
4. Pa PerkinElmer E Help 4 Menu Manual Voltage kV ER Capture Size 7 Small Large Current UA nu h Live Er w FOV mm 30 Ke Mal Scan Technique A Ki FT y gt M Q WARMUP REQUIRED Scan Settings Choose a pre set or custom scan configuration from this drop down list see page 19 for more on preset configurations or page 21 for details on custom configuration set up Scan Parameters Scan parameter values specified by the selected scan setting Scan settings can be edited here but the changes are not saved to the system Available scan configurations see Table 4 3 on page 20 Scanner status Actual degree of gantry rotation Returns the gantry to the 0 degree rotation position To manually rotate the gantry prior to a scan select the degrees of rotation from the drop down list or enter a value and click Set Actual z axis position of the sample bed into or out of the bore Moves the sample bed to the O position and initiates manual control of the sample bed To move the sample bed in out of the bore select a distance mm from the drop down list or enter a value and click Se Closes the control software and if open the Database window 6 Quantum FX uCT Software User s Manual Chapter 2 Getting Started 7 2 3 System Shut Down Procedure PerkinElmer does not recommend power cycling the Quantum FX uCT turni
5. Click Browse b Select a database in the dialog box that appears and click OK c Click Connect Figure 3 3 Connecting to a Database Connect to Database a Browse For Folder Choose Database to Connect To D Advanced Training WIS U December Ba Computer Ma OS C Wa Data Di ei DVD RW Drive E Connect to Database In D Advanced Training IVIS U December 9 Quantum FX uCT Software User s Manual 3 3 Data Organization The image data series in a database are associated with a study and a sample Figure 3 4 A sample Chapter 3 Managing Databases may include multiple studies and a study may include one or more series Figure 3 4 Database Window File Sample Settings CELIT TIL ECE Language Help Database Location D test3 Database Description Study Study Description Series Path to Save New Data Series Description Birth Date Sex SampleName Sample 12 Study 20121112 Date of Last Update Obese Mouse 1 DOB 7 17 12 fem 20121023 DOB 7 7 12 femal 20121023 10 23 2012 None 10 23 2012 None 10 23 2012 None 10 23 2012 None 10 25 2012 None 10 25 2012 None 10 25 2012 None 10 25 2012 None 10 25 2012 None 10 25 2012 None 11 12 2012 None 10 23 2012 1 24 42 PM 10 23 2012 1 12 19 PM 10 23 2012 1 24 54 PM 10 23 2012 1 18 47 PM 10 23 2012 1 21 45 PM 10 23 2012 1 37 37 PM 10 23 2012 1 47 48 PM 10 23 2012 2 06 06 PM 10 25
6. Figure 3 9 b Select a folder in the dialog box that appears and click OK 5 Click Save 13 Quantum FX uCT Software User s Manual Chapter 3 Managing Databases 14 Figure 3 9 Copying a Database 5 We T r Save Database As LA Browse For Folder LX Database Name RE Desktop 153 Libraries B CT admin d B Computer PO System C xs Data D ei DVD RW Drive E DA DB Location Make New Folder Cancel Searching a Database 1 Click the KY toolbar button 2 Enter a text string choose the search options and click Search Figure 3 10 Database Search Parameters Advanced Search Settings Search by String String ta Find Select Search Columns Name Study Description Description Series Study Series Description Select Search Options Match Case Require Exact Match Search by Date Dates 1 1 2009 v 6 1 2012 le Choose Search Columns Date of Birth Date of Last Update El Date of Creation Search by Database ID ID D Quantum FX uCT Software User s Manual Chapter 3 Managing Databases 15 Reconstructing a Database In the rare event that a database is corrupted it 1s possible to reconstruct the database from the xml files in the CT image folders To reconstruct a database 1 Select File Rebuild Database on the menu bar 2 Select the database for reconstruction in the dialog box that ap
7. 2012 10 38 36 AM 10 25 2012 1 45 21 PM 10 25 2012 2 04 49 PM 10 25 2012 3 05 14 PM 10 25 2012 3 58 53 PM 10 25 2012 3 59 03 PM 10 25 2012 4 22 12 PM 11 12 2012 11 33 00 AM 11 12 2012 11 32 42 AM 11 12 2012 11 51 44 AM 11 12 2012 2 47 08 PM 11 12 2012 2 51 53 PM 10 23 2012 1 11 10 23 2012 1 12 10 23 2012 1 18 10 23 2012 1 18 10 23 2012 1 21 10 23 2012 1 25 10 23 2012 1 47 10 23 2012 2 06 10 25 2012 10 38 10 25 2012 1 45 10 25 2012 2 04 10 25 2012 3 05 10 25 2012 3 58 10 25 2012 3 59 10 25 2012 4 22 11 12 2012 11 3 11 12 2012 11 32 11 12 2012 11 5 11 12 2012 2 46 11 12 2012 2 51 Immediate Review AutoPlay 358 512 Scan Time 26sec 133256 133911 133623 Customizing the Database View You can select particular columns and data to display in the Database window To hide show columns 1 Right click a column header in the Database window Figure 3 5 2 Select Configure Display Columns on the shortcut menu that appears 3 Inthe dialog box that appears remove or add a check mark next to a column name that you want hide or show Click OK 10 Quantum FX uCT Software User s Manual Chapter 3 Managing Databases Figure 3 5 Select Database Columns ID Name Description Study Study Description Series Series Description Birth Date No Fiter 7 No Fiter Ir No Fiter Je E S 1 Initial BB tests 10 5 2010 a a a a a Ex Create New Study
8. Function c BL 08 D Click and drag to draw a measurement cursor on an image Right click a measurement cursor to delete the selected cursor or all cursors Draws a rectangular ROI on an image Right click an ROI to delete the selected ROI or all ROls Draws a circular ROI on an image Displays a line graph of pixel intensities along a line segment drawn on an image de 2 5 Select a slice view Click the Ej button The Line Profile window appears Press and hold the mouse button while drawing a line segment on the image The Line Profile graph shows the pixel intensities along the line segment Drag either end of the line segment to resize or reposition the line segment The graph is automatically updated Click the Ca button again to turn off and close the line profile graph Opens a dialog box that enables you to insert a comment on an image To add a comment to an image jm 2 Click the button 3 4 To resize or reposition the arrow drag the arrow tip or the arrow end To move the Select a slice view Enter text and click OK in the dialog box that appears arrow drag the entire arrow To delete a comment or all comments right click a comment and select a delete option from the shortcut menu E Add notes to an image Opens a Save As dialog box that enables export of the 3D reconstruction vox Copies the image to the system clipboard
9. Viewing Images Table 5 6 Partition Tools continued Tool Functions Adjusts the angle of the left and right portions of the partition If the top of the partition is narrow this can result in partition forming a point as shown For example Adjusts the partition height Adjusts the width at the bottom only For example te Adjusts the partition height and moves the left side of the partition For example gt Adjusts the partition height and moves the right side of the partition For example Managing Classified Data You can edit the color table and name that are assigned to different parts of the data and change the display order of multiple overlapping data parts For example if there are two data parts that overlap the 3DViewer displays the first part in the list on top of the second part To change the color table for particular data 1 Double click the part name and select Color on the shortcut menu 2 Select a color or define a custom color in the Color Palette that appears Click OK 45 Quantum FX uCT Software User s Manual Chapter 5 Viewing Images 46 Figure 5 7 Selecting a Color Table E Volume Rendering Control a s mem Se Rendering Selection Image control a 3DCOLOR iw o Component Selection v Bb Part 2 EJ mm JI Eon Color N 2 Rename H AN fe Delete wl 3DCOLOR Du ENEN RO E
10. a 201010052 Update Metadata T 20101005 3 Delete Entry 20101005 4 Set Image Save Location i zen 20101005 6 la Gsag 20101011 3 RingCal 20101011 To filter the data Select a filter from the Name Study and or Series drop down list Figure 3 6 Database Filters Description Study Study Description Series Series Description No Fitter 7 NoFiter 7 Ma Filter see 1 20100506 112006 113030 201 00806 2 201 008063 20100303 Sample 2 20100806 20100905 20100903f2 3 4 Managing Data Reconstructed image data vox can be imported between databases or exported from the database to another location such as the desktop Importing Data 1 Select a save location sample and study for the data in the Database window See page 17 for instructions on selecting a save location 2 Click the kd toolbar button Alternatively select File Import File on the menu bar 11 Quantum FX uCT Software User s Manual Chapter 3 Managing Databases 12 3 Select the data vox for import in the dialog box that appears and click Open The imported series appears in the Database window The original data name is listed in the series Description Exporting Data Select the series for export in the Database window 2 Click the 4 toolbar button Alternatively select File Export File on the menu bar 3 Inthe dialog box that appears Figure 3 7 confirm the defau
11. audible click when the safety interlock properly engages as the door is closed emm 3 Click the Warm up button e in the control panel 4 Click OK the warning message that appears Figure 4 2 Figure 4 2 Warm Up Warning Message Caution Warm up Caution X rays will be Produced When Energized Would you like to proceed If you would like to remove all objects from the chamber and CLOSE the door MID 1006 CAUTION Do not open the instrument door when X rays are being produced the control panel displays XRAY ON and the X ray indicator is flashing Opening the door terminates the X rays and aborts the warm up process The X ray tube begins the warm up process and generates X rays The time required for warm up depends on how long it has been since the instrument was last used Table 4 1 When warm up is completed the X ray tube status is STANDBY Figure 4 1 Table 4 1 Estimated Time Required for Warm Up Duration of Instrument Disuse Approximate Time Required for Warm Up 8 hours to one month 15 min One to three months 40 min More than three months 120 min 4 2 Select a Save Location All image data series are saved to a database where the data are organized by sample and study sample study series See page 10 for more details on data organization Before image acquisition select a database and specify the sample and study where the series will be sav
12. displays the 3D reconstruction Figure 4 13 See Chapter 5 on page 35 for more information on viewing 3D reconstructions Figure 4 11 CT Scan Confirmation Message Caution CT scan Caution X rays will be Produced When Energized Would you like to proceed Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition Figure 4 12 Control Panel and Xcapture Window During a Scan E Contre a ar SS Opens langage Hap PerkinElmer Mode aru aliaga KV Current wt BO 160 C Seal d Lace TV imm Tsing Technique Ei X ray tube status ON n Dep Painia Control decree X RAY COM Gantry position Help Nee MR Ti Self IH Level HIT 11 21 2012 1 4748 PM inzxcmiz20 amp 08PM 10 22 2012 206 hiasan 10 38 36 AM 1025 2512 10 58 puasana Lakan PM pidea 2704 48 PM 10 22 2012 2 52 53 PH NUDE 012 3 533 PW fin 25 2012 amp 2212 PM 10 25 2012 4 22 Iia 113340 AM 1112 2612 11 3 NAAN Re AM 1172 2012 11 3 Sample Nama Saepe 125 Shady 20121112 listened Date 21012 1 24 42 PM D ZV 2012 1 24 34 PM D 21 2212 1 351 PW 10 23 2012 1 11 Teu 118 15 23 2812 1 24 13 23 2012 NAT 10 25 2012 1 45 10 45 2012 21H08 TONE NGO 162522011138 10 25 2012 155 Das 3 405 14 PM j EX J imesedate Rewer l x EAY ON X ray tube status ON DH 3
13. on the method used to select the save location the Add Sample or Add Study dialog box may not automatically appear To display them right click a selected sample or study in the Database window and choose Update Data on the shortcut menu assigned by the software cannot be edited A sample identifier Figure 4 3 Enter Information About a New Sample and or New Study Add Sample ETE Add Study mxm Sample Study Series Sample Study Series ID Study 7 20100909 2 Name Study Description Description v Create Date 9 9 2010 Birth Date 9 9 2010 Ek Updated Date g 9 2010 Sex None Create Date 3 3 2010 Updated Date 3 9 2010 Required Required Add Cancel Add Cancel 18 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 19 4 3 Set Up Automatic Image Export After acquisition DICOM images can be automatically exported to a user selected location Select Setting Automatic DICOM Export Settings in the Database window 2 Puta check mark next to Export DICOM file after each scan in the dialog box that appears 3 Choose the File path or VOX folder option and click the Browse button to select a folder Click OK Figure 4 4 Automatic DICOM Export Settings Automatic DICOM Export Settings Export DICOM file after each scan File Export Location File path D VOX folder 4 4 Set the Scan Condi
14. 0 20 20 20 20 Live uA 80 80 80 80 80 80 80 80 80 80 80 80 80 80 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 73 73 60 60 30 30 40 40 73 73 24 24 20 20 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 Scan Time sl Std 17sec sl sl Fine 2min v sl Std 17sec E sl Fine 2min KA Std 26sec mi sl Fine 3min v Std 17sec sl Fine 2min ei zl Std 17sec sl Fine 2min ei sl Std 17sec ei sl Fine 2min ei sl Std 17sec E sl Std 17sec zl sl Std 17sec E Std 17sec mj Std 17sec Ej zl Std 17sec ml zl Std 17sec El zl Std 17sec ll sl Std 17sec sl Std 17sec ei sl Std 17sec ei sl Std 17sec Hi sl Std 17sec sl v Std 17sec El sl Std 17sec ml sl Std 17sec Hi Std 17sec mi Std 17sec E sl Std 17sec IS sl Std 17sec me To create a custom scan condition a Enter a name under the Menu Name column header b Enter values for kV CT uA and Live uA c Make a selection from the FOV and Scan Time drop down lists d Click Save OK The scan condition appears in the Mode drop down list in the Control panel To edit an existing scan condition a Double click a table cell and enter a new value b Select a new value from a parameter drop down list c Click Save OK The changes are saved to the system 4 Select the scan condition from the Mode drop down list in the Control panel 23 Quantum FX uCT Software U
15. ERE SUE EERE Define Custom Colors gt gt Cancel To edit a part name 1 Double click the part name and select Rename on the shortcut menu 2 Enter a name in the dialog box that appears Click OK To show hide or delete parts 1 To hide a part remove the check mark next to the part name 2 Puta check mark next to the name to show the part Figure 5 8 3 To delete a part double click the name and select Delete on the shortcut menu that appears Figure 5 8 Select Parts to Show or Hide e Volume Rendering Control o O Ex Preset Rendering Selection a B End iem Lu W ITE E E Del anh m Select the parts to display in the 3DViewer FJ LA EJ E ht 3DCOLOR DW Part 2 Quantum FX uCT Software User s Manual 3DViewer Display Options Chapter 5 Viewing Images You can adjust the detail level and shading that 1s used to render the 3D reconstruction in the 3DViewer 1 Click the button to access the tools for setting shading and detail level 2 Adjust the settings using the sliders Changing shade settings automatically updates the 3D Viewer display Table 5 7 Tool Box Settings Item Description Shader Setting Ambient Diffuse Specular Specular Power Controls the intensity of the ambient light that is applied to the rendering Setting range 0 0 to 1 0 dim to bright Sets the level
16. Image Acquisition Sometimes ring reduction may result in image artifacts Figure 4 21 The artifacts are usually minor However 1f they are unacceptable you can turn off ring reduction and repeat the acquisition Figure 4 21 Example Image Artifacts Resulting From Ring Reduction To turn off ring reduction 1 Select Options Ring Reduction Settings in the Control Panel Figure 4 22 2 Remove the check mark next to the scan technique that was used during acquisition and click OK Figure 4 22 Turning Off Ring Reduction E Control Language Help Pa PerkinElmer Menu Manual D o amp 8 Ring Reduction Settings Scan Technique Std 17sec Std 26sec Fine 2min Q STANDBY Voltage kV Current uA Fine 3min 0 0 Dyn 17secx2 a sl CT feo X Sync 34sec Capture Size Live 80 M 4 5min Small Large FOV mm 10sec Gating Technique 30 z 8 vw Scan Technique Maec Std 26sec M 2 5min s e Rotation Control degree al 0 Home pos Set Stage Control mm ow Initiakze Set Sa Ring Reduction m l I l I l I lt 1 I I 33 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 4 7 Perform Acquisition in Fluoroscopy Mode In fluoroscopy mode a range of user selected frames can be viewed as a movie scrolling th
17. Remove the subject from the sample chamber when the Quantum FX uCT is in Standby mode CAUTION Do not remove or change the bore cover until the Quantum FX pCT is in q standby mode and the CT scan button ex becomes available Figure 4 13 AutoViewer Pe dE View t Loupe Magnification L Seiting 3 Language iL Help Hj 27 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 28 D NOTE If the AutoViewer does not automatically appear confirm that the AutoView option is selected in the Database window CT Scan With Respiratory Gating IMPORTANT Click the emergency stop Q button in the control panel to abort acquisition and stop X ray generation 1 Click the respiratory K gating button 2 Turn on Live Mode by clicking the qe button in the Control panel The Xcapture window appears and shows the subject in real time Figure 4 14 Figure 4 14 Xcapture Window Respiratory gating is selected in this example Control clt ss II Xcapture Options Language Help File Options Display Help Pa PerkinElmer Image data bounding box Image data outside the Menu Manual Voltage kV Current uA x on bounding box are not used p z afe z Capture Size Live 80 m j t Ewe E m d ROI positioned over the FOV mm n RN diaphragm Gating Technique i z aa in the reconstruction Viewz1224 Respiratory synchroniza
18. T Software User s Manual Chapter 4 Image Acquisition 21 Table 4 3 Preset Scan Configurations continued Preset Scan kV CT pA Live pA FOV Length Scan Image Dynamic Bore Condition mm mm Time Pixel Size Scan Cover sec um Available FOV24 fine 90 160 80 24 20 120 50 no S FOV20 std 90 160 80 20 20 17 40 no 5 FOV20 fine 90 160 80 20 20 120 40 no S FOV10 std 90 160 80 10 10 26 20 no 5 FOV10 fine 90 160 80 10 10 180 20 no S Table 4 4 Scan Parameters Parameter Description kV The voltage requested from the X ray tube CT pA The current requested from the X ray tube Live LA The current requested from the X ray tube during fluoroscopy Live Mode scan FOV mm The field of view Scan Time The time that the gantry requires to rotate 360 degrees during image acquisition Custom Scan Conditions There are two ways to set custom scan conditions m Edit the scan parameters in the Control panel see below These changes are not saved to the system Or m Create and save a scan condition in the Menu Settings table see page 23 The custom scan condition will be available in the Menu drop down list of the Control panel Editing Scan parameters in the Control Panel Select Manual from the Menu drop down list 2 Enter a custom voltage and current in the Control panel Figure 4 6 Select a Preview Size FOV and Scan Technique See Table 4 5 for more details on these p
19. an IMage 44 000 100 8 Ze 93 39x am Eri D eR E Dar os PO E pod eg 34 Viewing Images ccce an 35 Previewing Dalta EEN 35 Cl ViCWeIS aah PAGKAALAM CG ee ee eo ee 36 PUOVICWEL 4 4 ae ork a X8 C9 CI RG kG o aio a ed oe p ee ee ER GE a dra 36 Viewer Optional Plugin 00 ee ee 37 3D Viewer Optional Plugin 0 ccc ee RI t tn 41 Classifying Image Data Using the 3D Viewer 43 Managing Classified Data 45 3DViewer Display OptionS 23 pawaaan wa wk Roe aci cac AN aR ewe cade des 4 UNAN AA ar a 48 1 Welcome About This Manual What s New in the Quantum Fx uCT Software on page 2 Quantum FX uCT Help on page 2 Additional Important Documentation on page 2 Technical Support on page 3 1 1 About This Manual Welcome to the Quantum FX uCT Software User s Manual The software controls the Quantum FX uCT instrument a micro computed tomography uCT scanner which provides high resolution high speed radiographic imaging of small animals and reconstruction of 3D volumetric data Please see the Quantum FX uCT System Manual part no 128059 Rev0A for information on the Quantum FX uCT instrument Figure 1 1 Quantum FX uCT Instrument Quantum FX uCT Software User s Manual 1 2 What s New in the Quantum Fx p CT Software a Acquire images with respiratory or cardiac gating m Preset scan conditions FOV40 std and FOV40 fine m 4 5 minute acquisition time fo
20. antum FX uCT software click the Pa icon on the desktop Figure 3 1 Database Window File Sample Settings Language Help Ozh eaa BY OB Database Location D Advanced Training IVIS U December Study Dez pin Seres Seres Description Date of Brih Sex Date of Last Update 12 6 2012 None 12 6 2012 257 10PM 1 12 6 2012 257 35 PM 12 6 2012 25954 PM 1 2 Click the New Database button Di in the Database window Alternatively select File New Database on the menu bar 3 In the dialog box that appears a Enter a name for the new database Figure 3 2 Quantum FX uCT Software User s Manual Chapter 3 Managing Databases b Click Browse and in the dialog box that appears navigate to the drive where the database will be saved and click OK c Click Create The new database appears in the Database window Figure 3 2 Creating a New Database fa Connect to Database Browse For Folder Choose Database to Connect To Advanced Training VIS U December Ba Computer gg OS C xis Data D 3 DVD RW Drive E Connect to Database In D Advanced Training WIS U December 3 2 Connecting to a Database Click the Connect to Database button g in the Database window 2 Ifthe database name is listed the dialog box that appears double click the name Alternatively select the database name and click Connect Figure 3 3 If the database name is not listed in the dialog box a
21. arameters Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition Figure 4 6 Setting Custom Scan Conditions E Control 2 amp 8 Options Language Help Pa Actual voltage output of the PerkinElmer Actual current output of the X ray X ray tube during a scan Menu Manual tube during a scan Voltage kV Current uA 0 IN 0 o cr 16o Select the current for the scan Capture Size Live 80 D Enter the voltage for the scan Small C Large GON mm DESS SERGE Select the current for a e I fluoroscopy Live Mode scan Q STANDBY Stage Control mm Table 4 5 Control Panel Acquisition Parameters Parameter Description Voltage The voltage affects the potential of the electron beam between the cathode and anode and therefore the energies in the X ray spectrum that is generated Current The current affects the amount of X rays that are generated and therefore the dose CT The current setting for a scan Live The current setting for a fluoroscopy Live Mode scan Capture Size Large or Size options for the Xcapture window Small FOV The field of view mm Scan Technique Std A common scan configuration These scans typically require 17 or 25 seconds Fine A scan mode that reduces image noise These scans typically require 2 or 3 minutes Dyn A scan configuration that performs two scans and s
22. e 36 Autoviewer on page 36 3D Viewer Optional Plugin on page 41 SimpleViewer on page 48 5 1 Previewing Data The Database window provides previews of 3D reconstructions Table 5 1 Previewing Data in the Database Window Select To Preview Sample The series from all studies under the sample Figure 5 1 Study All series in the study Series Series Figure 5 1 Previewing Data in the Database Window Scan conditions for the selected series 70 Ve 462 512 V Immediate Review AutoPlay uA FOV Scan Time 200 30 26sec 133311 Thumbnail of the series in the selection If there are multiple series in the selection click one of the thumbnails to display in the preview pane above Select the Immediate Review option to automatically display a 3D reconstruction in the AutoViewer after acquisition See page 36 for more details on the Autoviewer Choose the AutoPlay option to view a playback of the slices in the 3D reconstruction Uncheck the AutoPlay option and move the slider to view a particular slice Quantum FX uCT Software User s Manual Chapter 5 Viewing Images 36 5 2 CT Viewers View the data using one of the CT viewers Table 5 2 Table 5 2 CT Viewers Viewer Name Description See Page AutoViewer The AutoViewer automatically appears after a scan and 3D Below reconstruction are completed The Autov
23. ed You can save a series to a new or existing sample and a new or existing study within the sample uU NOTE The selected database drive must have at least 10GB free disk space available If this requirement is not met the scan will not proceed Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition Set the Save Location 1 Connect to a database or create a new database See Managing Databases page 9 for details 2 Follow the instructions in Table 4 2 to select a sample and study for the series Table 4 2 Setting the Save Location in the Database window To Save the Series to a Do One of the Following New sample and new study Click the Q toolbar button Or Right click the Database window and select New Sample on the shortcut menu Or Select Sample New Sample on the menu bar Existing sample and new study Select the sample row and click the LI toolbar button Or Right click the sample row and select New Study on the shortcut menu Or Select the sample row and select Sample New Study on the menu bar Existing sample and existing Select the study row and click the LI toolbar button study an Right click the study row and select Set Series Save Location on the shortcut menu 3 Enter the sample and or study information in the dialog box that appears Click Add For example edit the default sample name and enter a description of the sample H NOTE Depending
24. ftware User s Manual 1 5 Technical Support For technical support please contact us at Telephone 800 762 4000 US E mail Fax 1 203 925 4602 Global TechSupport PERKINELMER COM 1 203 944 4904 PerkinElmer US Corporate Headquarters 940 Winter Street Waltham Massachusetts 02451 USA Chapter 1 Welcome 3 2 Getting Started Workflow Overview System Startup Procedure on page 4 System Shut Down Procedure on page 7 2 1 Workflow Overview Table 2 1 presents an overview of acquiring CT data on the Quantum FX uCT scanner Table 2 1 Workflow overview Step See Page 1 Start the Quantum FX y CT control software click the Ke icon on the desktop See below 2 Warm up the Quantum FX uCT scanner click the button in the Control Panel 17 3 Create or select a database 8 9 4 Create or select a sample and study where the image data series will be saved 18 5 Set the scan conditions 19 6 Place the subject in the sample chamber and center the subject in the Xcapture window 19 7 Start the CT scan 26 8 View and analyze the 3D reconstruction 35 2 2 System Startup Procedure 1 Turn on the Quantum FX uCT workstation H NOTE This also powers on the Quantum FX uCT scanner 2 Double click the icon on the desktop to start the Quantum FX uCT software The Control Panel and Database window appear Figure 2 1 Figure 2 2 shows an overview of the Control panel functions All i
25. hapter 5 Viewing Images Table 5 5 Volume Rendering Controls continued Item Function gi Hides all voxels to the left of the x axis crosshair X axis crosshair Hides all voxels that are above the intersection of the x and y axes Adds removes voxels to the display after it has been cut using the a m Or E button After the 3D reconstruction has been cut in the x y or z plane click the Slice button To add or remove voxels from the display click and hold the mouse button while dragging the mouse across the image Ga Undo button that reverses the cuts that were made unhides the voxels Performs the undo action in a step by step reverse order the last cut is the first reversed and so on Opens a dialog box that enables you to export the 3DViewer display to a graphic file or a movie Classifying Image Data Using the 3D Viewer The 3DViewer initially displays image data with a default air noise boundary that identifies bone Use the volume rendering controls to create and visualize additional intensity ranges or parts for example a particular type of soft tissue The histogram in the volume rendering controls represents the distribution of voxel intensities in the 3D reconstruction and their color opacity values The goal of classification is to set color and opacity values for different intensity ranges so that regions of the volume that are of interest appear opaque and
26. he scan 30 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 31 8 Click Yes in the confirmation message that appears Figure 4 11 X rays are energized as indicated by the blinking voltage icon and the instrument status box Figure 4 12 The Xcapture window opens then gantry rotation and image acquisition begin Figure 4 18 CT Scan Confirmation Message Caution CT scan Caution X rays will be Produced When Enerqized Would you like to proceed ve Je Progress indicators for image processing appear Figure 4 19 The AutoViewer displays the 3D reconstruction Figure 4 13 after processing is complete See Chapter 5 on page 35 for more information on viewing 3D reconstructions Figure 4 19 Processing Progress for Images Corresponding to Diastolic and Systolic Phases of the Cardiac Cycle CJ GetSynchronizedRaw ID Type Study Senes Status Tw ER DIASTOLE 20130214 155008 diastole SYSTOLIC 20130214 155008 systole r uy Ring Reduction The ring reduction algorithm helps reduce image artifacts and is turned on by default Figure 4 20 shows example images of before and after ring reduction Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 32 Figure 4 20 Images With Example Ring Artifacts Before Ring Reduction After Ring Reduction Ring artifact Ring artifact Quantum FX uCT Software User s Manual Chapter 4
27. iewer enables you to a View 2D images slices in the x y or z planes a Select other image data vox for viewing a Print the current AutoViewer display Viewer An optional plugin that displays 2D image data Double click 37 a series in the Database window to open the data in the Viewer Alternatively select a series and click the Run Viewer toolbar button Il Use this viewer to visualize the 3D anatomical planes and perform basic 2D measurements 3D Viewer An optional plugin that enables rendering of a 3D 41 reconstruction classifying the data SimpleViewer Used to view image data that have been exported from a 48 database This viewer is used to interact with the 3D anatomical planes and make basic 2D measurements Additional plugins for example the optional 3D Viewer will not be accessible 5 3 Autoviewer H NOTE If the AutoViewer does not automatically appear after reconstruction confirm that the Immediate Review option is selected in the Database window Figure 5 1 Figure 5 2 AutoViewer hie Wee 9 Loupe Mugrehuabon l hang Lanquage l eda F Drag the crosshairs to select a slice location in the x y and z axis planes Alternatively use the middle mouse button to scroll through the slices within a viewing plane Quantum FX uCT Software User s Manual Chapter 5 Viewing Images 37 Table 5 3 AutoViewer Menu Commands Menu Co
28. lt name or enter a different name for the new folder where the data will be copied Figure 3 7 Export File Export File mm Export Settings Data will be copied to this folder File Format DICOM 16bit Single page Y NOTE Data will be exported into the folder located at New Folder Path New Folder Name locations listed above Image Slice Selection From To a All Slices D Limited 1 1512 Cancel To change the folder path click Browse and select a location in the dialog box that appears 5 Select a file format from the drop down list File Format Description CT image with a SimpleViewer Exports the 3D reconstruction vox along with the SimpleViewer See page 48 for more details on the SimpleViewer DICOM 16bit Single page Exports individual slices in a file formats common for medical imaging Tiff 16 Multi page Exporting to DICOM format creates a folder of dcm files one file per slice JPEG Exporting to Tiff format creates a single file which includes all of the slices Bitmap PNG AVI Exports the selected images in a video file format 6 Toexport only a subset of the slices contained in an image choose the Limited option and enter a range of slice numbers Click OK Deleting Data D NOTE Only the system administrator can delete a database includes the associated studies and series study includes the associated series or series only See page 15 f
29. m the Rotation Control drop down list b Click Set Figure 4 10 c If necessary use the stage X axis controls on the instrument front panel to center the subject in the Xcapture window Figure 4 10 25 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 26 7 Check the subject position in the Xcapture window at the 90 degree gantry position a Select 90 from the Rotation Control drop down list and click Set Figure 4 10 b If necessary use the stage Y axis controls on the instrument front panel to center the subject in the Xcapture window Figure 4 9 8 Click the 7 button to turn off Live Mode and close the Xcapture window H NOTE Live Mode automatically times out after 150 seconds 4 6 Perform a CT Scan This section explains how to perform a ua CT Scan Without Gating a CT Scan With Respiratory Gating on page 28 a CT Scan With Cardiac Gating on page 30 CT Scan Without Gating IMPORTANT Click the emergency stop Q button in the control panel to abort acquisition and stop X ray generation 1 Click the CT Scan button Ko to begin the scan 2 Click Yes in the confirmation message that appears Figure 4 11 X rays are energized as indicated by the blinking voltage icon and the instrument status box Figure 4 12 The Xcapture window opens then gantry rotation and image acquisition begin The 3D reconstruction automatically proceeds after acquisition is complete The Auto Viewer
30. mage data are saved to a database See Chapter 3 on page 8 for more details about databases U NOTE The user ID CTadmin has administrator privileges If you have any concerns during the startup procedure please contact PerkinElmer technical support see page 3 for assistance Chapter2 Getting Started 5 Quantum FX uCT Software User s Manual Figure 2 1 Control Panel and Database Window at Startup KC I QsX4GcGggaMID PerkinElmer Liadain Dale Desen Set Dest elee Brih Dale Sex sl DYAMI Nene E 2 201221148PM DAAM 211A TASS Hone 11 2002 LIIS PM 114201730 TLAV2012 Nene 12 11 2012 l24248 PM 11 11 2012 12 44 Control panel Database window Quantum FX uCT Software User s Manual Chapter 2 Getting Started Figure 2 2 Control Panel X Ray Tube Status Actual voltage and current of the X ray tube Cardiac or respiratory gating options see page 28 Warm up button Starts the X ray tube warm up When warm up is complete this button becomes the Live Mode button shown below 1 l y Live Mode button cop This button appears after warm up is complete Click the Live Scan button to view the subject in real time Live Mode automatically times out after 150 minutes SEN CT Scan button Starts the CT scan Emergency Stop button 2 Aborts the current operations for example the CT scan V Control Options Language
31. mmand Description File Import Opens a dialog box that enables you to select another vox file for viewing File Print Opens a dialog box that enables you to print the current AutoViewer display Setting CT number Opens a dialog box that enables you to calibrate the Hounsfield Unit scale adjustment Setting System Choose this option to view the function key associations for quickly changing Configuration the window and level settings for image viewing View Status Bar Choose this option to show the x y coordinates of the mouse arrow in the AutoViewer window as well as the opacity value VAL View Horizontal View Displays the x and y axis views in a vertical orientation E ne I pm d Ea e xs TA CA Leepumdi Tee D View Vertical View Displays the x and y axis views in a horizontal orientation E ETC lai Wee Las bagaman kamag lispsage ili bisig Pi Viewer Optional Plugin The Viewer provides tools for 2D image display and analysis To open data in the Viewer double click a thumbnail or series row in the Database window Multiple series can be open in the Viewer at the same time Quantum FX uCT Software User s Manual Chapter 5 Viewing Images 38 Figure 5 3 Viewer Window U8 viewer o mem File F View OI Loupe Magnification L Setting S Language L Help H
32. nel of the instrument to move the sample bed into the bore To do this press and hold the Fast button while you press the Z axis left or right arrow Figure 4 9 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition Figure 4 9 Quantum FX p CT Front Panel X ray irradiation Lamp Stage X axis Control Stage Y axis Control ma Rotate Drive Lamp Stage Z axis Control a Use the stage control arrows di m in the control panel Figure 4 10 Move the sample bed a specific distance 1 Click Initialize Figure 4 10 2 Enter a distance in mm and click Set Figure 4 10 Control Panel PerkinElmer Menu Manual Voltage kV Current uA ai Small C Large CT 160 e Live 80 e FOV mm Gating Technique 30 x Scan Technique Std 26sec Gantry position set to 0 degrees Use these controls to move the sample bed in or out of the bore Options Language Help PerkinElmer Menu Manual mM Voltage kV Current uA o0 DI CT 160 e 1 Live 80 Small C Large coy mm Gating Technique 30 ba A Ki Scan Technique Std 26sec m Gantry position set to 90 degrees 6 Check the subject position in the Xcapture window at the 0 degree gantry position a Select O fro
33. ng the system components on and off If it is necessary to shut down the scanner for any reason it is important to follow the procedure below Make sure that all processes are finished Confirm that the gantry and sample bed are not moving 2 Close the Control panel and Database window If prompted save any data Turn off the computer using the standard Windows shut down procedure This also shuts down the Quantum FX uCT scanner 4 Turn off the power to the other system components and power surge protection devices If you have any concerns during the shut down procedure please contact PerkinElmer technical support see page 3 for assistance H NOTE The Emergency Stop button is not intended as a main X ray source control and should not be used to turn the X ray function ON or OFF on a routine basis lt should only be used in the unlikely situation where the X ray source must be immediately turned OFF 3 Managing Databases Creating a Database Connecting to a Database on page 9 Data Organization on page 10 Managing Data on page 11 Managing Databases on page 13 System Administrator Login Logout on page 15 3 1 Creating a Database All image data series are saved to a local database Each scan is stored in the folder D Data and the raw acquisition data are stored in Computer Data D The database facilitates interacting with and managing data sets To create a database 1 Open the Database window by starting the Qu
34. ns Display Help Jr Image data bounding box Image data outside the bounding box are not used in the reconstruction Menu Manual Voltage kV Current uA E ct fieo Live 80 DI Capture Size Small C Large FOV mm Gating Technique 20 Position the ROI over the apex of the heart and diaphragm Scan Technique 45min ss 5min Y e X eS d X RAY ON Rotation Control otation Control degree T NI 1 NG Views 740 tl Respiratory synchronization 2620 0 mS ICH Set EN EI EI Diaphragm motion signals Cardiac motion signals 4 o o In the Xcapture window adjust the ROI dimensions to position it over the apex of the heart and diaphragm Rotate the gantry 90 degrees Ensure that the subject is within the filed of view and the ROI is correctly positioned Rotate the gantry back to 0 degree position Check the respiratory and cardiac signal trace in the Respiratory synchronization window Figure 4 14 The large trace spikes represent diaphragm movement The smaller spikes in between represent cardiac movement Ensure that the cardiac signal is as visible as possible Figure 4 17 It may be possible to improve the signal visibility by adjusting the ROI position Wait for the breath rate to stabilize with longer than 1000 ms 1 sec between breaths Click the CT Scan button x to begin t
35. of focus of the simulated light on the rendering Setting range 1 most focused resulting in the brightest rendering 0 the dimmest Affects the lens that is used for light in the rendering Setting range O to 1 0 dim to bright Affects the lens used for the visual rendering Setting range O to 50 The results are dependent on the Specular setting Level of Detail Still Level of Detail Moving Level of Detail Sets the quality of the visual rendering that is still not moving Highest quality 1 0 Decreasing this number reduces the quality of the rendering and also reduces the computational burden Sets the quality of the visual rendering during rotation translation or zooming The highest quality is set relative to the still quality Decreasing this number will reduce the quality of the rendering during movement and can be used to speed up reformatting of the rendering 47 Quantum FX uCT Software User s Manual 5 5 SimpleViewer Chapter 5 Viewing Images The Simple Viewer 1s included with image data that has been exported from a database It provides tools for 2D image display and analysis To view data in the SimpleViewer 1 2 Open the folder with the exported image data Double click the file Simple Viewer exe The Simple Viewer appears and displays the image data The Image Control Label Filter and Measure options in the SimpleViewer are identical to those in
36. on again to return to the default gray scale color table Show or hide the x and y axis crosshairs Show or hide a scale bar in the windowpanes Toggles between a horizontal or vertical slice orientation Resets to the default slice view or the default display if the image has been rotated translated or scaled Masks all voxels with gray scale value below the threshold value entered in the field Click the 189 button to turn the mask off or on Specifies a range of grayscale values for image display Modify the range by editing the values in the fields Click the 77 button to turn the feature off or on Filter Air Bal jx When a mask is applied using the Q button generates a purple mask click the button to mask additional voxels at the edges of the mask This can help sharpen visualization at edges such as around the animal skin When a mask is applied using the 3 button generates a green mask click the button to remove single pixel noise rrom the thresholded mask Enables you to select a 3D filter that removes noise by combining pixels and displaying the average intensity of the selected pixels ORIGINAL Does not apply a filter SOFT Applies a 3 x 3 x 3 averaging filter SMOOTH Applies a 5 x 5 x 5 averaging filter Measure 39 Quantum FX uCT Software User s Manual Chapter 5 Viewing Images Table 5 4 Viewer Functions continued ei o 3
37. or instructions on system administrator login logout Quantum FX uCT Software User s Manual Chapter 3 Managing Databases CAUTION Deleting data removes all reconstructed and raw images from the system The images cannot be recovered once the delete process is initiated 1 Select a sample study or series in the Database window 2 Right click the row and select Delete Data on the shortcut menu 3 Click Yes in the confirmation message that appears Figure 3 8 Deleting Data Data List ID Mame Descriptian Study Study Description Ser les Series Description No Fite Isi No Filter No Filter gt Sample 1 20100806 201 00806 2 201 OO80E 3 20100903 Update Data 20100904 Delete Data 3 201005042 Set Series Save Location 201009043 20100504 4 20100305 112006 New Sample Mew Study set Display Columns Sample 9 5 ample 3 S ample 4 3 5 Managing Databases Copying a Database Copying a database provides a convenient way to share data H NOTE Only the system administrator can copy a database See page 15 for instructions on system administrator login logout 1 Connect to the database that you want to copy See page 9 for details on connecting to a database 2 Select File Save Database as on the menu bar 3 Enter a name for the new database in the dialog box that appears 4 To change the save location a Click Ref
38. p gt PerkinElmer Quantum FX uCT Imaging System User s Manual March 2013 PN 128055 Rev01 2013 PerkinElmer Health Sciences All right reserved PN 128055 Rev01 PerkinElmer Health Sciences 68 Elm Street Hopkinton MA 01748 Telephone 508 435 9761 or 508 435 9500 FAX 508 435 9761 E mail Global Techsupport PerkinEImer com Website WWW PerkinElmer com Contents Chapter 1 Chapter 2 Chapter 3 Chapter 4 WCIGOING 6 654225 6 5 AKA KAKA ER EE E ee ee E eee aes 1 ABUEG TINS E TC WEEN 1 What s New in the Quantum Fx uCT Software aaa 2 Quantum FX CT Help uuo d naka dac d ent eg hahaha kan Rmuk AN Ee AR e KA 2 Additional Important Documentation een 2 Technical SUDORE aure du doi OE BG MA r tua PP CT A eee Ram PP d ear 3 Getting Started 2533 x dm xx BAUAN GARA X xtd e 4 Workflow Overview su cac cuc a ox Eo MAN Ee Ro ed Rz ee 38 Rd RR ORC a 4 System Startup Procedure 4 System Shut Down Procedure eee ha 7 Managing Databases c c 8 Creating a Database ee nnns 8 Connecting to a Database EN daw ied x ode ACA X CX do C ORC CAR ed Cac 9 Data Organization esse saaan aana EPUPREQCESI2e32443 Pee eked 3 PAX PES EFE ed 10 Customizing the Database View 10 J iEnhrenab cdgPTrrPr 11 Iniporting d Ed ances ooh see ese REA Ee HEUS RES ae eA tae MUR dS did 11 EXPOLING Dala 2226556 ama bene IEEE ha ESO p qan
39. pears and click OK Deleting a Database H NOTE Only the system administrator can copy a database See page 15 for instructions on system administrator login logout Do not delete a database using Windows Explorer CAUTION Deleting a database removes all reconstructed and raw images from the system The images cannot be recovered once the delete process is initiated 1 Connect to the database to be deleted a Click the Connect to Database button e in the Database window b Select the database in the dialog box that appears 2 Select File Delete Database on the menu bar Click OK In the confirmation messages that appears 3 6 System Administrator Login Logout Select Settings Login Logout as Administrator on the menu bar 2 Enter the administrator password in the dialog box that appears The default password is ctadmin 3 Click Login or Logout if logging out Figure 3 11 Login as Administrator Login as Administrator Password f Y paceman Login Cancel 4 Image Acquisition Instrument Warm Up Select a Save Location on page 17 Set the Scan Conditions on page 19 Place a Subject in the Sample Chamber on page 24 Perform a CT Scan on page 26 Perform Acquisition in Fluoroscopy Mode on page 34 4 1 Instrument Warm Up Check the Control panel to see if the instrument requires warm up Figure 4 1 If the Control panel is not open click the Pa icon on the desktop Fig
40. r FOV20 FOV24 FOV40 FOV60 and FOV73 m Ability to search the database Automatically export images from the database 1 3 Quantum FX yCT Help To view a tooltip about a button function put the mouse cursor over the button 1 4 Additional Important Documentation Chapter 1 Welcome Table 1 1 lists other important documentation related to the use of the Quantum FX uCT instrument Table 1 1 Documentation for the Quantum FX uCT instrument Procedures for the Operation of the Quantum FX uCT Cabinet X Ray System features operating procedures and emergency procedures for the Quantum FX uCT instrument Document Name Description Part No Quantum FX uCT System Manual Provides detailed instructions on the safe 128059 operation and maintenance of the Ouantum FX UCT instrument Safe Operating and Emergency Provides detailed instructions on the safety 128054 128634 Canada Mouse Imaging Shuttle Instructions Explains how to install and use the optional Mouse Imaging Shuttle that can be used to contain the subject during optical and CT imaging The Mouse Imaging Shuttle enables imaging and transfer of subjects between imaging platforms without disrupting the subject position As a result 3D optical and 3D volumetric data can be precisely registered 127820 RevA Quick Start Guide Aquiring Images on the Quantum uFX CT Instrument Quick reference guide for image acquisition Quantum FX uCT So
41. rg uo oe Eur mod 12 Deleting Data sue 292923 BAOG NAN DA MI NAMATAAN DUMADAAN ANO EE saws 12 Managing Databases eere nnns 13 Copying a Database hh hh nnns 13 Searching a Database 0 hr 14 Reconstructing a Database es 15 Deleting a Database 448242422448 66 4064 0 RE Rey RORG E SR RA RS Rok ABS ESS 15 System Administrator Logomn logout 15 Image Acquisition clc as 16 Instrument Warm Up 20s ac ac mre bet S e RU TD ed DOSE pcd ce o de Pc Te SECURE TR OR d we ER 16 Select a cave LOCOLON uoa moe AM KA MAKA EE E MAG MAGA E en 17 Set Up Automatic Image Export es 19 oet the Scan Conditions a3 3 2 a 5 MA 8 9 4 7 Cd ea OR be AB KANA OR Oe KALAM ea 19 Preset Scan ConditionS s xo aca age oe dice ac eee X ee Ee Re X CHR EC c aed 19 Custom Scan Conditions 454 a ba d ba gk eR oci NEE ENKE E AE AG 21 Place a Subject in the Sample Chamber ces 24 ESH Orr Gl SCAN maagawan ahh MAKA MG MANG KA NG BA MEE E ird UR ER ORI REO 26 CI Scan Without Gating nasawi ueuPezscaxmRezes4speszee342254 9 24 26 CT Scan With Respiratory Gating uude amp ee ew ee Be Rae oce eco d 28 CT Scan With Cardiac Gating i us ance edu 98 83 15 3er din eec el p do n d MAGKA c aeu i 30 RINO Hed DTE lt c2 046 5 pud edu ea x PE qu eue Ea cse IW 31 Perform Acquisition in Fluoroscopy Mode teen eens 34 Quantum FX uCT Software User s Manual Contents Chapter 5 Saving
42. rough 2D images and stored in the image database Confirm the current save location or select a new save location see page 17 for details 2 Placethe subject in the sample chamber and set the scan conditions See Set the Scan Conditions page 19 and Set the Scan Conditions page 19 for more details 3 In the X Capture window move the slider to the first frame of the movie and click Start Figure 4 23 Move the slider to the last frame of the movie and click End 4 Click Play to scroll through the selected frames 5 Click Movie to save the frames as a video The movie is saved to the current save location Figure 4 23 Xcapture Window and Options for Acquisition and Viewing Xcapture eJ uu EA 2DViewer control 83 Configuration f e x MT Image control Measure i ie Eb O A Brightness amp Contrast ES Control Brightness Contrast Ranae oh Views 795 795 X 487 Y 334 Level 3477 795 795 Movie Photo Play tog V Auto Brightness Control slider Select acquisition and viewing options from the Xcapture window Options menu Saving an Image A single frame in the Xcapture window can be saved as a snapshot and stored in the database 1 Select a frame using the slider in the Xcapture window 2 Click Photo The snapshot is saved to the current save location 34 5 Viewing Images Previewing Data CT Viewers on pag
43. ser s Manual Chapter 4 Image Acquisition 24 4 5 Place a Subject in the Sample Chamber The Quantum FX uCT is ready to acquire images after instrument warm up is complete See page 16 for more details on instrument warm up Install the appropriate bore cover See Table 4 3 on page 20 2 Place the anesthetized subject on the sample bed See the Quantum FX uCT System Manual part no 128059 for instructions If using the Mouse Imaging Shuttle place the shuttle with the anesthetized subject on the sample bed If needed connect the gas anesthesia tubing See the Mouse Imaging Shuttle Instructions part no 127820 for details on the Mouse Imaging Shuttle 3 Push the sample table into the bore and slide the instrument door closed so that the interlock properly engages 4 Turn on Live Mode by clicking the gg button in the Control panel The Xcapture window appears and shows the subject in real time Figure 4 8 H NOTE Only the image data inside the bounding box are used to reconstruct the 3D volume Figure 4 8 Xcapture Window Respiratory gating is selected in this example Xcapture fo els File Options Display Help Image data bounding box Image data outside the bounding box are not used in the reconstruction Gating bounding box positioned around the diaphragm Views 1 533 5 5 Move the sample bed into the bore using any of the following methods m Use the stage Z axis controls on the front pa
44. the Viewer See Table 5 4 on page 38 for details Figure 5 9 SimpleViewer S A SimpleViewer File F View V Loupe magnification L Set Start a a ing S Language L Help H ID study Series Image control PESA Oo ae amp Bl Bis Filter mj me ZZ zb Measure i z Ss e ss 48
45. tion Image Ist image 2nd image 8 Mix image Start the scan after the breath rate is stable and greater than 1000 ms 3 In the Xcapture window adjust the ROI dimensions to position it over the diaphragm 4 Rotate the gantry 90 degrees Ensure that the subject 1s within the filed of view and the ROI is correctly positioned over the diaphragm 5 Rotate the gantry back to 0 degree position 6 Check the respiratory signal trace in the Respiratory synchronization window Figure 4 14 Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 29 Trace spikes represent diaphragm movements Wait for the breath rate to stabilize with longer than 1000 ms 1 sec between breaths Figure 4 14 7 Click the CT Scan button x to begin the scan Click Yes in the confirmation message that appears Figure 4 11 X rays are energized as indicated by the blinking voltage icon and the instrument status box Figure 4 12 The Xcapture window opens then gantry rotation and image acquisition begin Figure 4 15 CT Scan Confirmation Message Caution CT scan Caution X rays will be Produced When Energized Would you like to proceed 9 Review the Mix Image results in the Respiratory Synchronization window Figure 4 16 The goal is to achieve a trace that 1s as flat as possible If necessary adjust the Ratio or Offset see Table 4 6 Figure 4 16 Respiratory Synchronization Windo
46. tions To set the scan conditions choose a m Preset scan condition or specify custom scan parameter conditions in the control panel Gating option if performing a gated CT scan Preset Scan Conditions 1 Make a selection from the Mode drop down list Figure 4 5 Quantum FX uCT Software User s Manual Figure 4 5 Selecting a Preset Scan Condition d Control Options Language Help PerkinE mer Menu Manual V Vol FOV4O fine FOV24 std FOV24 fine FOV20 std FOV20 fine FOV O std Captul FOV1 O fine EE Gating Technique 60 e sp Scan Technique Std 17sec v Q STANDBY Rotation Control degree GER o Home pos NG Stage Control mm Paa a sl Table 4 3 Preset Scan Configurations Chapter 4 Image Acquisition Preset Scan kV CT pA Live pA FOV Length Scan Image Dynamic Bore Condition mm mm Time Pixel Size Scan Cover sec um Available FOV73 std 90 160 80 73 60 1 148 yes L M S FOV73 fine 90 160 80 73 60 120 148 yes L M S FOV60 std 90 160 80 60 60 17 118 yes L M S FOV60 fine 90 160 80 60 60 120 118 yes L M S FOV30 std 90 160 80 30 30 26 59 no L M S FOV30 fine 90 160 80 30 30 180 59 no L M S FOV40 std 90 160 80 40 40 17 80 no M S FOV40 fine 90 160 80 40 40 120 80 no M S FOV24 std 90 160 80 24 20 17 50 no S 20 Quantum FX uC
47. titches them together to increase the axial field of view After the first scan the bed moves into the bore and the second scan is completed The software uses the images from both scans to generate the 3D reconstruction vox 22 Quantum FX uCT Software User s Manual Creating a Custom Scan Condition Chapter 4 Image Acquisition Create a custom scan condition by editing an existing scan condition or creating a new scan condition 1 Select Options Preset Modes on the Control panel menu bar The Menu Settings table appears It lists the available scan conditions and their parameter settings Figure 4 7 Preset Mode Settings E M Control Lal Options Language Help 4 amp Service Menu La Login Logout Imer Menu Manual D Voltage kV Current uA 90 e CT 160 v Capture Size Live 80 Small Large FOV mm Gating Technique 30 z Scan Technique 3 x e Q STANDBY Rotation Control degree 9 EM Home pos Stage Control mm FOV 3 fine FOV60 std FOV60 fine FOVS3O std FOV30 fine FOVAO std FOV40 fine FOV24 std FOV24 fine FOV20 std FOV20 fine FOV10 std FOV10 fine 90 90 90 90 90 90 90 90 90 90 90 90 90 90 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 160 160 160 160 160 160 160 160 160 160 160 160 160 160 20 20 20 20 20 20 20 20 20 20 20 20 2
48. unimportant regions are hidden the voxels are transparent Quantum FX uCT Software User s Manual Chapter 5 Viewing Images 44 Figure 5 5 Voxel Histogram Ma Volume Renkant Control T Preset Rendering Selection 1 r Image Control Voxel intensity naasa 3DCOLOR i Bone Click to resize the histogram X axis Voxel color table and opacity Click the Log button to switch the histogram between a linear or log Y axis To classify a part of the data 1 Click the Add Part button amp Figure 5 6 A new partition appears in histogram The new part name is added to the part list Figure 5 6 Adding a Part to the Histogram A Volume Rendering Control D EJ Preset Rendering Selection EN control End coment T 4 E E kk ei CI Component Selection Bone Bret 2 Partition tools NS E e Part list mg 9o E g 3DCOLOR DW Bone Click to add a partition New Part2 2 Modify the partition to visualize the tissue of interest using the tools partition tools Table 5 6 To use a tool a Click the button then click the histogram b Press and hold the mouse button while dragging the mouse left right or up down Table 5 6 Partition Tools Tool Functions Moves translates the partition up down or left right on the histogram Quantum FX uCT Software User s Manual Chapter 5
49. ure 4 1 Control Panel Warm Up Required Warm Up in Progress Warm Up in Complete X rays are OFF X rays are ON X rays are OFF Quantum FX UCT is ready to acquire images Control Lee Options Language Help PerkinElmer Menu Manual D Voltage kV Current uA 0 0 o0 DI CT 160 e Capture Size Live 80 D Small Large Control Options Language Help Pa PerkinE imer Control Options Language Help PerkinElmer Menu Manual r Voltage kV Current uA eiitmg9iis Menu anual Voltage kV Current uA 72 100 90 Jil creo z Capture Size Live E Small Large o0 DI CT 160 DI r Capture Size Live 80 DI Small Large FOV mm FOV mm FOV mm ag 30 z Gating Technique Gating Technique 30 Scan E Scan Technique x e Std IESESSS a CG WARMING UP STANDBY Live Mode button appears when warm up is complete Warm up button Rotation Control degree Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition 17 To warm up the instrument 1 Confirm that the sample chamber is empty no subject or sample bed is inside the sample chamber 2 Close the instrument door H NOTE The Quantum FX iCT instrument does not generate X rays unless the door is properly closed and the safety interlock is engaged There is an
50. w Example Mix Image Respiratory synchronization GH Image 3 lst image 5 2nd image o Mix image Mix Ratio 35 X Offset 5 N Close and Reconstruction Table 4 6 Respiratory Synchronization Item Description 1st image Image acquired during the first gantry rotation 2nd image Image acquired during the second gantry rotation Mix image Image produced by combining and smoothing the first and second images Ratio The width of a single breath relative to the interval between breaths Offset A measure of how far to shift the breath center relative to the peak center Close and Reconstruction Click to close the XCapture window and reconstruct the image 10 Click Close and Reconstruction after obtaining a satisfactory Mix Image result The 3D reconstruction proceeds The AutoViewer displays the 3D reconstruction Figure 4 13 See Chapter 5 on page 35 for more information on viewing 3D reconstructions Quantum FX uCT Software User s Manual Chapter 4 Image Acquisition CT Scan With Cardiac Gating 1 2 IMPORTANT Click the emergency stop PD button in the control panel to abort acquisition and stop X ray generation Click the cardiac a gating button Turn on Live Mode by clicking the qe button in the Control panel The Xcapture window appears and shows the subject in real time Figure 4 14 Figure 4 17 Xcapture Window V Control Options Language Help File Optio
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