Editing Scanco User Instructions (section)

=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.  
*Log sheets are to remain in the lab.  If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]


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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===
Regardless of what cast is used, the X-, Y-, and Z- dimensions remain the same:
*X=14cm
*Y=14cm
*Z=designated 20cm distance in the scanner

Standard Scanco Distal Radius Cast
*Used for distal radius scans of 1-3 stacks.  Designed with the hand to be in a curved position.  The field-of-view allows for scanning of approximately the most distal 1/4 of the forearm.
Standard Scanco Distal Tibia Cast
*Used for distal tibia scans of 1+ stacks.  Designed with the foot to be in a flexed (upright) position.  The field-of-view allows for scanning of approximately the most distal 1/4 of the tibia.
Standard Scanco Sample Holder
*This is a cylindrical tube with a cut-out window on the top.  
*Allows for scanning small ex-vivo and other samples.  The tube provides support for the sample during scanning.  
*Also used for in-vivo scans of the hand along with a platform that conforms to the hand and slides into the tube.  
Elbow Holder
*Used for scans of the elbow.  Designed to support the forearm during scanning.
Knee Holder
*A long cylinder cast cut in half lengthwise and with a foot holder at the end.  This cast is designed to slide over the gantry tongue, placing the leg further into the gantry, in order to scan at distances closer to the core of the body.
*Used for distal femur and proximal tibia (i.e. knee) scans.
*Used for mid-shaft tibia scans.
*Used for larger ex-vivo and other samples.

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file. 

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality. 


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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate). 
*Yellow tube samples holders are made of PEI (poly-ether-imide). 
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant 
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant 
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant 
|-
! scope="row"| Alcohols
|limited resistance
|resistant 
|-
! scope="row"| Bleach
|non resistant
|resistant 
|}


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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.  
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40. 
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]


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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP. 
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.


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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']] 
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP. 
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.


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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.  
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions. 


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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;" 
|- 
! scope="row"|  Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]] 
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]] 
|[[File:VivaCT40.jpg|135px]] 
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo 
Horizontal static patient setup 
|colspan="2"| Preclinical in vivo animal studies 
Horizontal static animal setup 
|colspan="2"| High resolution ex vivo specimen scans 
Vertical rotational sample setup 
|-
! scope="row"| E (KVp)
| 68 || 60 
|colspan="3"| 45, 55, 70  
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54 
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al 
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al 
| Fixed 0.5mm Al 
| Air, LE1~LE6, HE1~HE6, 
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L 
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0 
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50 
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]] 
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]] 
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]] 
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}


Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project. 

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.


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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter. 

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.


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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;" 
|-
! scope="col"| 
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68 
| 60 
| 70  
| 55 
| 45 
|-
! scope="row"| I (µA)
| 1470 
| 900 
| 114, 57
| 145, 72 
| 177, 88  
|-
! scope="row"| Power (W)
| 100 
| 54 
|colspan="3"| 8, 4 
|}

*'''Filter''':  Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3.  For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling. 


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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.


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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality.  To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol *  Scan Length in unit of mGy-cm.


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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;" 
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"|   High  
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}


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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;" 
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}


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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;" 
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}


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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;" 
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}


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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;" 
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}


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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.


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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors. 
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two. 
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness


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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.  

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).  
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number.  Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window.  An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).  
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.  
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button. 
#*As the first scan, a measurement number is assigned for this new scan.  Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].  
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:  
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.  
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40. 
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email.  Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.


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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.  
:*For uCT scanners: When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans.  You should not rescan the sample if there is a ring artifact.
:*For XtremeCT scanners: A small number of rings artifacts are expected and acceptable.  For a 168-slice scan, ring artifacts present in <5 slices total is acceptable.  If you observe ring artifacts in a larger number of slices, notify a staff member.  Do not repeat scans for ring artifacts.  In most cases, it is also unnecessary to perform a correction to already acquired data. 
<div><ul> 
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''


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