Media 000158880: Stained Head
Restricted Download
Type Volumetric Image Series
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
USNM:BIRDS:USNM 635813 Nothura maculosa
Managed by
Chris Milensky

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Media produced from the same original imaging that created Media 000158880 (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
000158880
Media type
Volumetric Image Series
Object element or part
stained head
Object represented
USNM:BIRDS:USNM 635813
Object taxonomy
Nothura maculosa
Object organization
NMNH - Division of Birds
Side
--
Orientation
--
Short description
--
Full description
Migrated MorphoSource 1 Media Group Title: HRXCT scan Migrated MorphoSource 1 Media File Description: University of Texas High-Resolution X-ray CT Facility Archive 2937\\r\\n\\r\\nLi:\\r\\ncrypt: Scans of an iodine-stained head of Northura maculosa (USNM 635813) for Zhiheng Li of UT DOGS. Specimen scanned by Matthew Colbert 15 February 2013. \\r\\n\\r\\n16bit: 1024x1024 16-bit TIFF images. II, 180 kV, 0.3 mA, intensity control off, high-power mode, no filter, empty container wedge, no offset, slice thickness 1 line ( = 0.07283 mm), S.O.D. 209 mm, 1400 views, 2 samples per view, inter-slice spacing 1 line ( = 0.07283 mm), field of reconstruction 68 mm (maximum field of view 68.52635 mm), scanner offset 5000, reconstruction offset 6000, reconstruction scale 3500. Acquired with 31 slices per rotation and 25 slices per set. Ring-removal processing done by Julia Holland based on correction of raw sinogram using IDL routine “RK_SinoRingProcSimul” with parameters “sectors=100, omit_edge=150.” Reconstructed with beam-hardening coefficients [0, 0.85, 0.05]. Deleted first 3 and last 3 duplicate slices from each rotation. Rotation correction processing done by Julia Holland using IDL routine “DoRotationCorrection.” Deleted first 25 blank slices. Post-reconstruction ring correction applied by Julia Holland with parameters “oversample=3, binwidth=9, sectors=60.” Total final slices = 1725.\\r\\n
Creator
--
Date created
--
Date uploaded
August 28, 2020

FILE OBJECT DETAILS Field Definitions

File name
16bit.zip
File format(s)
ZIP archive, TIFF
File size
2.46 GB
Image width
1024
Image height
1024
Color space
BlackIsZero
Color depth
16
Compression
Uncompressed
X pixel spacing
0.066410
Y pixel spacing
0.066410
Z pixel spacing
0.072830
Pixel spacing units
Mm
Slice thickness
--
Number of images in set
1,725

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
Zeiss Xradia microXCT-400, The University of Texas High-Resolution X-ray Computed Tomography Facility (University of Texas at Austin)

OWNERSHIP AND PERMISSIONS Field Definitions

Data managed by
Chris Milensky
Data uploaded by
Barbara Sulbaran
Publication status
Restricted Download
Download reviewer
Chris Milensky; Jessie Maisano
IP holder
Smithsonian Institution, National Museum of Natural History
Copyright statement
 In Copyright - Non-Commercial Use Permitted
Creative Commons license
 Creative Commons BY-NC-SA Attribution-NonCommercial-ShareAlike 4.0 International
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
Gordon and Betty Moore Foundation Grant 4498, NSF DBI-1902242
Publisher
--
Cite as
Migrated MorphoSource 1 Media Citation Instructions: Julia Clarke and Zhiheng Li provided access to these data , with data collection funded by the Gordon and Betty Moore Foundation Grant 4498 and data upload to MorphoSource funded by NSF DBI-1902242. The files were downloaded from www.MorphoSource.org, Duke University.
Media preview mode
--
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
 ark:/87602/m4/M158880
MorphoSource DOI
Not assigned
External identifier
--
External media URL
--

IMAGE ACQUISITION AND PROCESSING IN DETAIL

STEP 1: IMAGE ACQUISITION

Physical object USNM:BIRDS:USNM 635813 was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Zeiss Xradia microXCT-400
Device facility
The University of Texas High-Resolution X-ray Computed Tomography Facility (University of Texas at Austin)
Creator
Matthew Colbert
Event date
--
Software
--
Description
--
Description attachment
None
Reference attachment
None
Exposure time
--
Flux normalization
No
Pixel spacing calibration
--
Shading correction
No
Frame averaging
2
Projections
1400
Voltage
180
Power
--
Amperage
300
Surrounding material
empty container
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 000158880: Stained Head [CTImageSeries] [Etc] (this media).

Processing Details Field Definitions

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

Media produced by this event on MorphoSource

Media 000158880: Stained Head [CTImageSeries] [Etc] (this media)