Media 000504896: Aboral Half Of The External Plates
Restricted Download
Type Mesh
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen

Media Display

In Collections

GENERAL DETAILS Field Definitions

Media ID
000504896
Media type
Mesh
Object element or part
Aboral half of the external plates
Object represented
Object taxonomy
Hyperoblastus sp.
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 aboral half. Combined with 000504902 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
1-half_1__Multiple_Segs_.stl
File format(s)
STL
File size
367 MB
Points
3847536
Polygons
7697744
Map type
--
UV coordinates
False
Vertex color
False
Bounding box dimensions
1.355, 1.081, 1.382
Centroid coordinates
-0.215, 0.418, -0.166
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)
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
Data uploaded by
Publication status
Restricted 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
--
Cite as
--
Media preview mode
Interactive/Embeddable
Additional usage agreement
None

IDENTIFIERS AND EXTERNAL LINKS Field Definitions

MorphoSource ARK
MorphoSource DOI
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
TOMCAT Beamline X02DA
Device facility
Swiss Light Source (Paul Scherrer Institut)
Creator
--
Event date
--
Software
--
Description
--
Description attachment
Reference attachment
None
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

STEP 2: IMAGE PROCESSING

Raw Media 000490275: Theca [CTImageSeries] [CT] was processed with 3 activities to create derived Media 000504896: Aboral 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

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 000504896: Aboral Half Of The External Plates [Mesh] [CT] (this media)