Media 000398145: Premaxilla
Open Download
Type Mesh
Modality X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen

Media Display

In Collections

GENERAL DETAILS Field Definitions

Media ID
000398145
Media type
Mesh
Object element or part
premaxilla
Object represented
Object taxonomy
Mambawakale ruhuhu
Side
Right
Orientation
--
Short description
Right Premaxilla of Mambawakale ruhuhu - NHMUK R36620
Full description
3D mesh model of the Right Premaxilla of Mambawakale ruhuhu - NHMUK R36620 - unit: meter
Creator
Vincent Fernandez
Date created
July 21, 2021
Date uploaded
November 25, 2021

FILE OBJECT DETAILS Field Definitions

File name
Mambawakale_ruhuhu_-_NHMUK_R36620_-_01_PMX_R.stl
File format(s)
STL
File size
9.29 MB
Points
96065
Polygons
194832
Map type
--
UV coordinates
False
Vertex color
False
Bounding box dimensions
0.072, 0.092, 0.147
Centroid coordinates
0.369, -0.020, -0.184
Units of point coordinates
--

IMAGE ACQUISITION AND PROCESSING AT A GLANCE Field Definitions

Number of parent media
2
Number of processing events
3 (8 steps)
Modality
X-Ray Computed Tomography (CT/microCT)
Device
Nikon Metrology HMX ST 225, NHMUK Imaging and Analysis Centre (The Natural History Museum, London)

OWNERSHIP AND PERMISSIONS Field Definitions

Data uploaded by
Publication status
Open Download
IP holder
The Trustees of the Natural History Museum, London
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
© The Trustees of the Natural History Museum, London
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 NHMUK:PAL:PV R 36620 was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
X-Ray Computed Tomography (CT/microCT)
Device
Nikon Metrology HMX ST 225
Device facility
NHMUK Imaging and Analysis Centre (The Natural History Museum, London)
Creator
Vincent Fernandez
Event date
May 30, 2018
Software
Nikon Metrology Inspect X 3.1
Description
Tomogram of the skull resulting from the merging of 3 dataset (as the specimen was too large)
Description attachment
None
Reference attachment
None
Exposure time
1 second
Flux normalization
No
Pixel spacing calibration
--
Shading correction
Yes
Frame averaging
4
Projections
3142
Voltage
225 kV
Power
135 W
Amperage
600 μA
Surrounding material
foam
X-ray tube type
Nikon 225 UltraFocus
Target type
Reflection
Detector type
Scintillator (Phosphor used)
Detector pixels X
2000
Detector pixels size X
0.2
Detector pixels Y
2000
Detector pixels size Y
0.2
Detector configuration
Area (single or tiled detector)
Source object distance
744.05 mm
Source detector distance
1173.8 mm
Target material
Tungsten
Rotation number
--
Phase contrast
No
Optical magnification
No
Acquisition type
Sequenced

STEP 2: IMAGE PROCESSING

Raw media (undeposited) was processed with 7 activities to create derived Media 000392226: Skull Of Mambawakale Ruhuhu Nhmuk R36620 [CTImageSeries] [CT].

Processing Details Field Definitions

Creator
Vincent Fernandez
Event date
August 08, 2021
Software
Nikon Metrology Inspect X 6
Description
The dataset is a 16-bit stack of tomograms resulting from the merging of 3 individual dataset. Dataset 1 and 2 were acquired by moving the sample holder motor on the vertical axis; dataset 3 was acquired after turning the specimen upside down
Description attachment
None

Processing Activity 1: Reconstruction

Software
Nikon metrology inspect X
Description
Acquisition #1 and #2 reconstructed as 32-bit vol files

Processing Activity 2: Align Parts

Software
GNU Octave 5
Description
Alignment of dataset #1 and #2 based on motor position and refined based on image analysis

Processing Activity 3: Merge

Software
GNU Octave 5
Description
Merging of dataset #1 and #2 with a weighted averaging for the overlapping part

Processing Activity 4: Bit Depth Change

Software
GNU Octave 5
Description
Change of bit depth of dataset #1 and #2 32-bit to 16-bit based on manually selected min and max values

Processing Activity 5: Reconstruction

Software
Nikon metrology inspect X
Description
reconstruction of dataset #3 as a 16-bit volume, using the same min and max define earlier for dataset #1 and #2

Processing Activity 6: Align Parts

Software
VGstudiomax (Volume Graphics)
Description
Manual alignment of dataset #1+2 and #3

Processing Activity 7: Merge

Software
VGstudiomax (Volume Graphics)
Description
export of the aligned volume as a single 16-bit stack of tiff

STEP 3: IMAGE PROCESSING

Processing Details Field Definitions

Creator
Vincent Fernandez
Event date
July 21, 2021
Software
Blender
Description
Mesh models of the skull bones of Mambawakale ruhuhu - NHMUK R36620
Description attachment
None

Media produced by this event on MorphoSource

STEP 4: IMAGE PROCESSING

Derived Media 000392233: Complete Skull [Mesh] [CT] was processed with 1 activity to create derived Media 000398145: Premaxilla [Mesh] [CT] (this media).

Processing Details Field Definitions

Creator
Vincent Fernandez
Event date
July 21, 2021
Software
VGstudiomax
Description
3D mesh model of the right premaxilla of Mambawakale ruhuhu - NHMUK R36620
Description attachment
None

Processing Activity 1: Reconstructed Tomography to Mesh

Software
VGstudiomax
Description
Same process describe as parent ID media, but for a single bone

Media produced by this event on MorphoSource

Media 000398145: Premaxilla [Mesh] [CT] (this media)