Media 000612335: Whole Body
Open Download
Type Volumetric Image Series
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
SIO:Marine Vertebrates:67-272 Alloclinus holderi
Managed by
Ben Frable

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Media produced from the same original imaging that created Media 000612335 (this media). Includes all media associated with this media through an imaging and processing workflow.

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GENERAL DETAILS Field Definitions

Media ID
000612335
Media type
Volumetric Image Series
Object element or part
whole body
Object represented
SIO:Marine Vertebrates:67-272
Object taxonomy
Alloclinus holderi
Object organization
SIO Marine Vertebrate Collection
Side
--
Orientation
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Short description
HRXCT scan - whole body
Full description
University of Texas High-Resolution X-ray CT Facility Archive 1025 Rowe: Alloclinus: Scans of the head and whole body of Alloclinus holderi (SIO 67-272; captured Dec. 1, 1967 from Santa Catalina Island: Church Rock (33deg 23.0'N, 118deg 24.0'W)) for Dr. Lawrence Frank of UC San Diego, Dr. Timothy Rowe of the Department of Geological Sciences, The University of Texas at Austin, and DigiMorph. Specimen scanned by Matthew Colbert 25 May 2004. body/16bit: 512x512 16-bit TIFF images. II, 180 kV, 0.133 mA, no filter, empty container wedge, no offset, slice thickness 2 lines (= 0.042 mm), S.O.D. 61.1 mm, 800 views, 2 samples per view, inter-slice spacing 2 lines (= 0.042 mm), field of reconstruction 19.98 mm (maximum field of view 19.98355 mm), reconstruction offset 11300, reconstruction scale 2000. Acquired with 15 slices per rotation. Drift- and ring-removal processing done by Rachel Racicot based on correction of raw sinogram data using IDL routines “RK_SinoDeDrift” with parameter “driftlength=21, goodfile=300”, and “RK_SinoRingProcSimul” with parameters “binwidth=21, bestof5=21”. Total slices = 1560. The specimen was scanned in two parts. The scans were integrated by Rachel Racicot. Slice 300 from the head scan was placed into the body set to achieve similar levels when doing the drift correction. Slices from the head scan were reduced to 512x512 in IDL, and rotated 0.5o counter-clockwise in Photoshop to match with the slices from the second scan. Slice number 559 is the first slice from the body (second) scan.
Creator
Matthew Colbert
Date created
May 25, 2004
Date uploaded
March 15, 2024

FILE OBJECT DETAILS Field Definitions

File name
16bitrot.zip
File format(s)
ZIP archive, TIFF
File size
321 MB
Image width
258
Image height
489
Color space
BlackIsZero
Color depth
16
Compression
Uncompressed
Series type
Reconstructed image stack
X pixel spacing
0.039000
Y pixel spacing
0.039000
Z pixel spacing
0.042000
Pixel spacing units
Mm
Slice thickness
--
Number of images in set
1,560

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
Varian Medical Systems (Bio-Imaging Research, Inc) ACTIS CT scanner with FeinFocus X-ray source, The University of Texas High-Resolution X-ray Computed Tomography Facility (University of Texas at Austin)

OWNERSHIP AND PERMISSIONS Field Definitions

Data managed by
Ben Frable
Data uploaded by
Theresa De Cree
Publication status
Open Download
Download reviewer
Ben Frable; Jessie Maisano
IP holder
University of California
Copyright statement
 No Copyright - Non-Commercial Use Only
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
Encouraged But Not Required
Funding attribution
DBI-1902242, IIS-0208675
Publisher
oUTCT PEN
Cite as
Funding for scanning was provided by NSF grant IIS-0208675 to Tim Rowe. Data upload to MorphoSource was funded by DBI-1902242. The files were downloaded from www.MorphoSource.org, Duke University.
Media preview mode
Interactive/Embeddable
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
 ark:/87602/m4/612335
MorphoSource DOI
Not assigned
External identifier
--
External media URL
https://digimorph.org/specimens/Alloclinus_holderi/whole/

IMAGE ACQUISITION AND PROCESSING IN DETAIL

STEP 1: IMAGE ACQUISITION

Physical object SIO:Marine Vertebrates:67-272 was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Device facility
The University of Texas High-Resolution X-ray Computed Tomography Facility (University of Texas at Austin)
Creator
--
Event date
May 25, 2004
Software
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Description
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Description attachment
None
Reference attachment
None
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Flux normalization
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Pixel spacing calibration
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Shading correction
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Frame averaging
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STEP 2: IMAGE PROCESSING

Raw media (undeposited) was processed to create derived Media 000612335: Whole Body [CTImageSeries] [CT] (this media).

Processing Details Field Definitions

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

Media produced by this event on MorphoSource

Media 000612335: Whole Body [CTImageSeries] [CT] (this media)