Media 000164669: Head
Restricted Download
Type Volumetric Image Series
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
sama:R:unreg Varanus rosenbergi
Managed by
Marc Jones

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Related Media (1)

Media produced from the same original imaging that created Media 000164669 (this media). Includes all media associated with this media through an imaging and processing workflow.

Other Related Media (1)

Other media associated with the original imaging that produced Media 000164669 (this media) excluding those listed above. For example, could include derived media produced from children of this media (grandchildren) or other derived media produced from the top parent of this media (sibling or cousin).

Mesh
ยท Restricted Download

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GENERAL DETAILS Field Definitions

Media ID
000164669
Media type
Volumetric Image Series
Object element or part
Head
Object represented
sama:R:unreg
Object taxonomy
Varanus rosenbergi
Object organization
South Australian Museum Australia provider for OZCAM
Side
--
Orientation
--
Short description
MicroCT volume files (TIFF stack)
Full description
specimen? 16171? Migrated MorphoSource 1 Media File Title: MicroCT volume files (TIFF stack) Migrated MorphoSource 1 Media Group Title: Micro-CT volume and derivative mesh files Migrated MorphoSource 1 Media File Description: [System]\\r\\nScanner=Skyscan1076\\r\\nInstrument SN=19\\r\\nHardware=B\\r\\nSecure mode=OFF\\r\\nSoftware=Version 2. 6 (build 5)\\r\\nHome Directory=C:Skyscan1076\\r\\nTube=Hamamatsu 100/250\\r\\nCamera=Hamamatsu Orca-HRF\\r\\nCamera Pixel Size (um)= 11.31\\r\\nCamera X/Y Ratio=0.9923\\r\\n[Acquisition]\\r\\nData Directory=F:ResultsMarcEHJonesVar_rosen_headVar_rosen_head2\\r\\nFilename Prefix=Var_rosen_head_2nd\\r\\nSource Voltage (kV)= 100\\r\\nSource Current (uA)= 90\\r\\nFilter=Al 0.5 mm \\r\\nObject to Source (mm)=121.000\\r\\nCamera to Source (mm)=161.000\\r\\nNumber Of Files= 351\\r\\nNumber Of Rows= 524\\r\\nNumber Of Columns= 1968\\r\\nOptical Axis (line)= 200\\r\\nImage Pixel Size (um)= 34.0000\\r\\nImage Format=TIFF\\r\\nDepth (bits)=16\\r\\nData Offset (bytes)= 264\\r\\nHorizontal overlap (pixel)=32\\r\\nCamera horizontal position=Center\\r\\nVisual Camera=OFF\\r\\nScreen LUT=0\\r\\nExposure (ms)= 158\\r\\nRotation Step (deg)=0.600\\r\\nFrame Averaging=On (2)\\r\\nScanning position=55.650 mm\\r\\nSuggested beam-hardening correction=10\\r\\nSuggested HU-Calibration=2780\\r\\nNumber of connected scans=6\\r\\nNumber of lines to be reconstructed=411\\r\\nUse 360 Rotation=NO\\r\\nRotation Direction=CC\\r\\nScanning Trajectory=ROUND\\r\\nType Of Motion=STEP AND SHOOT\\r\\nCamera Offset=ON\\r\\nScanning Start Angle=210.000\\r\\nStudy Date and Time=Aug 05, 2016 14:51:10\\r\\nScan duration=01:07:00\\r\\n[Reconstruction]\\r\\nReconstruction Program=NRecon\\r\\nProgram Version=Version: 1.7.4.2\\r\\nProgram Home Directory=C:SkyScan\\r\\nReconstruction engine=GPUReconServer\\r\\nEngine version=Version: 1.7.4\\r\\nReconstruction from batch=Yes\\r\\nPostalignment Applied=1\\r\\nConnected Reconstruction (parts)=6\\r\\nSub-scan post alignment [0]=-0.500000\\r\\nSub-scan post alignment [1]=0.000000\\r\\nSub-scan post alignment [2]=1.000000\\r\\nSub-scan post alignment [3]=0.000000\\r\\nSub-scan post alignment [4]=0.000000\\r\\nSub-scan post alignment [5]=0.000000\\r\\nSub-scan scan length [0]=411\\r\\nSub-scan scan length [1]=412\\r\\nSub-scan scan length [2]=410\\r\\nSub-scan scan length [3]=411\\r\\nSub-scan scan length [4]=411\\r\\nSub-scan scan length [5]=411\\r\\nUsed extra rotation per scan(deg)= 0.000 0.000 0.000 0.000 0.000 0.000 \\r\\nUsed extra shift in X per scan(micron)= 0.000 51.244 69.152 152.475 203.823 254.726 \\r\\nUsed extra shift in Y per scan(micron)= 0.000 16.909 67.102 18.830 34.113 46.736 \\r\\nReconstruction servers= 5PBX622 \\r\\nDataset Origin=Skyscan1076\\r\\nDataset Prefix=Var_rosen_head_2nd~05\\r\\nDataset Directory=HERPNASCT_ScansScansREPTILESLizardsVaranidaeVaranusrosenbergiVar_ros_head2\\r\\nOutput Directory=HERPNASCT_ScansScansREPTILESLizardsVaranidaeVaranusrosenbergiVar_ros_head2Var_rosen_head_2nd_Rec\\r\\nTime and Date=Oct 16, 2018 19:29:48\\r\\nFirst Section=85\\r\\nLast Section=2474\\r\\nReconstruction duration per slice (seconds)=0.340467\\r\\nTotal reconstruction time (2056 slices) in seconds=700.000000\\r\\nSection to Section Step=1\\r\\nSections Count=2390\\r\\nResult File Type=BMP\\r\\nResult File Header Length (bytes)=1134\\r\\nResult Image Width (pixels)=1336\\r\\nResult Image Height (pixels)=1336\\r\\nPixel Size (um)=34.00320\\r\\nReconstruction Angular Range (deg)=210.60\\r\\nUse 180+=OFF\\r\\nAngular Step (deg)=0.6000\\r\\nSmoothing=1\\r\\nSmoothing kernel=0 (Asymmetrical boxcar)\\r\\nRing Artifact Correction=15\\r\\nDraw Scales=OFF\\r\\nObject Bigger than FOV=ON\\r\\nReconstruction from ROI=ON\\r\\nROI Top (pixels)=1697\\r\\nROI Bottom (pixels)=360\\r\\nROI Left (pixels)=313\\r\\nROI Right (pixels)=1650\\r\\nROI reference length=1968\\r\\nFilter cutoff relative to Nyquist frequency=100\\r\\nFilter type=0\\r\\nFilter type description=Hamming (Alpha=0.54)\\r\\nUndersampling factor=1\\r\\nThreshold for defect pixel mask (%)=0\\r\\nBeam Hardening Correction (%)=44\\r\\nCS Static Rotation (deg)=0.00\\r\\nCS Static Rotation Total(deg)=-210.91\\r\\nMinimum for CS to Image Conversion=0.007000\\r\\nMaximum for CS to Image Conversion=0.080000\\r\\nHU Calibration=OFF\\r\\nBMP LUT=0\\r\\nCone-beam Angle Horiz.(deg)=30.914574\\r\\nCone-beam Angle Vert.(deg)=8.421809\\r\\nAutomatic matching in Z=50\\r\\nAutomatic matching in X/Y=50\\r\\nAutomatic matching in rotation=5.000000\\r\\nAutomatic fusion=1\\r\\n[File name convention]\\r\\nFilename Index Length=4\\r\\nFilename Prefix=Var_rosen_head_2nd_rec\\r\\n
Creator
--
Date created
--
Date uploaded
October 09, 2020

FILE OBJECT DETAILS Field Definitions

File name
Var_ros_TIFFS.zip
File format(s)
ZIP archive, BMP
File size
885 MB
Image width
1336
Image height
1336
Color space
--
Color depth
8
Compression
0; None; BI_RGB
X pixel spacing
0.034003
Y pixel spacing
0.034003
Z pixel spacing
0.034003
Pixel spacing units
Mm
Slice thickness
--
Number of images in set
2,390

IMAGE ACQUISITION AND PROCESSING AT A GLANCE Field Definitions

Number of parent media
0
Number of processing events
1 (0 steps)
Modality
X-Ray Computed Tomography (CT/microCT)
Device
Bruker SkyScan 1076 with modified camera, Adelaide Microscopy (University of Adelaide)

OWNERSHIP AND PERMISSIONS Field Definitions

Data managed by
Marc Jones
Data uploaded by
Marc Jones
Publication status
Restricted Download
Download reviewer
Marc Jones
IP holder
Marc Jones
Copyright statement
--
Creative Commons license
--
Morphosource use agreement type
Standard
Permits commercial use
Commercial Use Not Permitted
Permits 3D use
3D Printing Limited
Required archival of published derivatives
On MorphoSource
Funding attribution
--
Publisher
--
Cite as
--
Media preview mode
Interactive/Embeddable
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
 ark:/87602/m4/M164669
MorphoSource DOI
Not assigned
External identifier
--
External media URL
--

IMAGE ACQUISITION AND PROCESSING IN DETAIL

STEP 1: IMAGE ACQUISITION

Physical object sama:R:unreg was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Device facility
Adelaide Microscopy (University of Adelaide)
Creator
Mark Hutchinson
Event date
--
Software
--
Description
--
Description attachment
None
Reference attachment
None
Exposure time
--
Flux normalization
No
Pixel spacing calibration
--
Shading correction
No
Frame averaging
--
Projections
--
Voltage
100
Power
--
Amperage
90
Surrounding material
--
X-ray tube type
--
Target type
--
Detector type
--
Detector pixels X
--
Detector pixels size X
--
Detector pixels Y
--
Detector pixels size Y
--
Detector configuration
--
Source object distance
--
Source detector distance
--
Target material
--
Rotation number
--
Phase contrast
--
Optical magnification
--
Acquisition type
--

STEP 2: IMAGE PROCESSING

Raw media (undeposited) was processed to create derived Media 000164669: Head [CTImageSeries] [CT] (this media).

Processing Details Field Definitions

Creator
Mark Hutchinson
Event date
--
Software
--
Description
--
Description attachment
None

Media produced by this event on MorphoSource

Media 000164669: Head [CTImageSeries] [CT] (this media)