Media 000436216: Whole Fish
Open Download
Type Volumetric Image Series
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
Managed by

Media Display

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Project
ยท Public

TAGS

GENERAL DETAILS Field Definitions

Media ID
000436216
Media type
Volumetric Image Series
Object element or part
Whole fish
Object represented
Object taxonomy
Phyllopteryx taeniolatus
Side
--
Orientation
--
Short description
Weedy seadragon entire body scan
Full description
Weedy seadragon Xradia scan of the full body at a 54uM voxel size.
Creator
--
Date created
--
Date uploaded
April 25, 2022

FILE OBJECT DETAILS Field Definitions

File name
seadragon_wholebody_tiff.zip
File format(s)
ZIP archive, TIFF
File size
6.54 GB
Image width
918
Image height
5683
Color space
BlackIsZero
Color depth
16
Compression
Uncompressed
X pixel spacing
54.000000
Y pixel spacing
54.000000
Z pixel spacing
54.000000
Pixel spacing units
Um
Slice thickness
--
Number of images in set
1,301

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 620, Knight Campus X-ray Imaging Core Facility (University of Oregon)

OWNERSHIP AND PERMISSIONS Field Definitions

Data managed by
Data uploaded by
Publication status
Open Download
Download reviewer
IP holder
--
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
PNAS
Cite as
Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes. Clay Small, Hope M. Healey, Mark C. Currey, Emily A. Beck, Julian Catchen, A. Lin, William A. Cresko, Susan Bassham. PNAS. 2022.
Media preview mode
Interactive/Embeddable
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
MorphoSource DOI
Not assigned
External identifier
--
External media URL
--

IMAGE ACQUISITION AND PROCESSING IN DETAIL

STEP 1: IMAGE ACQUISITION

Physical object UO:PTA:01 was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Zeiss Xradia 620
Device facility
Knight Campus X-ray Imaging Core Facility (University of Oregon)
Creator
--
Event date
--
Software
Dragonfly Pro
Description
The male seadragon was fixed in formalin and imagined in segments with the Zeiss Xradia 620 Versa. The voxel size was 20uM, energy was 80 kV, power was 10W, objective was .4X, and binning of 2. 4 wide field scans and 2 vertical stitch scans were taken and then reconstructed with Dragonfly pro.
Description attachment
None
Reference attachment
None
Exposure time
--
Flux normalization
--
Pixel spacing calibration
--
Shading correction
--
Frame averaging
--
Projections
--
Voltage
80kV
Power
19W
Amperage
--
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 000436216: Whole Fish [CTImageSeries] [CT] (this media).

Processing Details Field Definitions

Creator
--
Event date
--
Software
Dragonfly Pro
Description
Separate scans were stitched together with Dragonfly. For the dataset registration, the course rotation and translation was 2 degrees and 110 uM respectively with fine rotations and translations of .4 degrees and 11uM. The 3D stitching parameters were as followed weighted blending, nearest interpolation, and most precise resolution.
Description attachment
None

Media produced by this event on MorphoSource

Media 000436216: Whole Fish [CTImageSeries] [CT] (this media)