Media 000504902: Basal Half Of The External Plates
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Type Mesh
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
cmc:IP 37404 Hyperoblastus sp.
Managed by
Nidia Alvarez Armada

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Related Media (26)

Media produced from the same original imaging that created Media 000504902 (this media). Includes all media associated with this media through an imaging and processing workflow.

Parent Media (Top And Direct)

The media that was processed to create Media 000504902 (this media). The media immediately preceding this media in the imaging and processing workflow. Also the media closest to what was produced from original imaging or the media with the least amount of derived processing.

CTImageSeries
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Other Related Media (25)

Other media associated with the original imaging that produced Media 000504902 (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).

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GENERAL DETAILS Field Definitions

Media ID
000504902
Media type
Mesh
Object element or part
Basal half of the external plates
Object represented
cmc:IP 37404
Object taxonomy
Hyperoblastus sp.
Object organization
CMC Vertebrate Paleontology Department
Side
--
Orientation
--
Short description
Reconstruction of the external plates of Hyperoblastus reimanni. This object divides the external plates vertically in half to facilitate the visualisation of the internal organs, this is the basal half. Combined with 000504896 create the entire reconstruction of the external plates.
Full description
--
Creator
Nidia Álvarez-Armada
Date created
September 01, 2020
Date uploaded
March 20, 2023

FILE OBJECT DETAILS Field Definitions

File name
2-half_2__Multiple_Segs_.stl
File format(s)
STL
File size
343 MB
Points
3597548
Polygons
7195248
Map type
--
UV coordinates
False
Vertex color
False
Bounding box dimensions
1.316, 1.194, 1.317
Centroid coordinates
-0.213, -0.336, -0.220
Units of point coordinates
--

IMAGE ACQUISITION AND PROCESSING AT A GLANCE Field Definitions

Number of parent media
1
Number of processing events
1 (3 steps)
Derived directly from
Media 000490275: Theca [CTImageSeries] [CT]
Modality
X-Ray Computed Tomography (CT/microCT)
Device
TOMCAT Beamline X02DA, Swiss Light Source (Paul Scherrer Institut)

OWNERSHIP AND PERMISSIONS Field Definitions

Data managed by
Nidia Alvarez Armada
Data uploaded by
Nidia Alvarez Armada
Publication status
Restricted Download
Download reviewer
Nidia Alvarez Armada
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
--
Cite as
--
Media preview mode
Interactive/Embeddable
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
 ark:/87602/m4/504902
MorphoSource DOI
 10.17602/M2/M504902
External identifier
--
External media URL
--

IMAGE ACQUISITION AND PROCESSING IN DETAIL

STEP 1: IMAGE ACQUISITION

Physical object cmc:IP 37404 was imaged to create raw Media 000490275: Theca [CTImageSeries] [CT].

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Device facility
Swiss Light Source (Paul Scherrer Institut)
Creator
--
Event date
--
Software
--
Description
--
Description attachment
Description Attachment
Reference attachment
None
Filter
--
Exposure time
600 ms
Flux normalization
--
Pixel spacing calibration
--
Shading correction
--
Frame averaging
--
Projections
1501
Voltage
37keV
Power
--
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
Yes
Optical magnification
--
Acquisition type
--

Media produced by this event on MorphoSource

Media 000490275: Theca [CTImageSeries] [CT]

STEP 2: IMAGE PROCESSING

Raw Media 000490275: Theca [CTImageSeries] [CT] was processed with 3 activities to create derived Media 000504902: Basal Half Of The External Plates [Mesh] [CT] (this media).

Processing Details Field Definitions

Creator
Nidia Álvarez-Armada
Event date
September 01, 2020
Software
SPIERS
Description
The fossil specimen was imaged with synchrotron tomography using the TOMCAT (TOmographic Microscopy and Coherent rAdiology experimenTs) beamline of the Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland. The specimen was scanned with a voltage of 37 keV, 1501 projections each with an exposure time of 600 ms, using the 2x objective. The tomographic datasets were used to digitally reconstruct the internal anatomy of the specimen using the SPIERS software suite (Sutton et al. 2012). This was achieved by creating three-dimensional virtual models of the internal structures in SPIERSedit. The reconstruction was based on 2480 slices, with segments assigned to structures with different brightness values, corresponding to variation in X-ray attenuation (correlated with material density) within the sample.
Description attachment
Description Attachment

Processing Activity 1: Background Removal and/or Masking

Software
SPIERSedit
Description
2480 slices with a generated range of four thresholds (threshold 1, 60−82; threshold 2, 82−120; threshold 3, 120–144; threshold 4, 144−255) for the 26 masks represented in the .stl file.

Processing Activity 2: Image and/or Mesh Compression

Software
SPIERSedit
Description
Down sampling value in axes X, Y and Z of 2

Processing Activity 3: Smoothing/Noise Reduction

Software
SPIERSview
Description
Tiny island removal

Media produced by this event on MorphoSource

Media 000504902: Basal Half Of The External Plates [Mesh] [CT] (this media)