Media 000668788: Skull Block
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Type Volumetric Image Series
Modality Synchrotron Imaging
Media represents biological specimen
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GENERAL DETAILS Field Definitions

Media ID
000668788
Media type
Volumetric Image Series
Object element or part
Skull block
Object represented
Object taxonomy
Heterodontosaurus tucki
Side
--
Orientation
--
Short description
Skull and cervical vertebrae
Full description
Image of the skull and cervical vertebrae in a single angular block
Creator
Vincent Fernandez
Date created
--
Date uploaded
October 06, 2024

FILE OBJECT DETAILS Field Definitions

File name
CONCAT_HA-1000_21.80um_160keV_AM-4766_skull_0_pagnorm_holo_-0.30_0.65_jp2-10_crop_.zip
File format(s)
ZIP archive
File size
13.6 GB
Image width
--
Image height
--
Color space
--
Color depth
--
Compression
--
Series type
Reconstructed image stack
X pixel spacing
21.800000
Y pixel spacing
21.800000
Z pixel spacing
21.800000
Pixel spacing units
Um
Slice thickness
21.8

IMAGE ACQUISITION AND PROCESSING AT A GLANCE Field Definitions

Number of parent media
0
Number of processing events
1 (0 steps)
Modality
Synchrotron Imaging
Device
ESRF Beamline ID17, European Synchrotron Radiation Facility (European Synchrotron Radiation Facility)

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
DSI-NRF African Origins Platform 98825; DSI-NRF African Origins Platform 98800; DSI-NRF Centre of Excellence in Palaeosciences; Palaeontological Scientific Trust; Durand Foundation for Evolutionary Biology and Phycology
Publisher
--
Cite as
--
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 am:4766 was imaged to create undeposited raw media.

IMAGING DETAILS Field Definitions

Modality
Synchrotron Imaging
Device facility
European Synchrotron Radiation Facility (European Synchrotron Radiation Facility)
Creator
Vincent Fernandez
Event date
--
Software
--
Description
Specimen AM 4766 was imaged on the ID17 beamline of The European Synchrotron (ESRF, Greno- ble, France). The experiment consisted of two parts: (1) imaging the whole of each block and (2) re- imaging specific regions of interest at higher resolution (i.e., the sternal region where anatomy is obscured by matrix and larger parts of the skeleton). The beamline was setup for propagation phase-contrast synchrotron X-ray micro-computed tomography: a monochromatic beam of 160 keV (Laue double bent Si 111), a sample-detector distance of 11 m and an indirect detector comprising a 2 mm LuAG scintillator, a set of lenses with a magnification of ~0.3􏰁, and a visible light detector (CCD or sCMOS). For the first set of experiments, we used a FReLoN 2k camera (ESRF), recording 4998 radiographs over a 360 ̊ rotation of the sample with a pixel size of 46.95 mm. Each radiograph consisted of five accumulated images, each with an exposure time of 40 ms, resulting in a total expo- sure time of 0.2 s per recorded radiograph. For the second part of the experiment, we used a PCO. edge 5.5 sCMOS with camera link (PCO, Kelheim, Germany), recorded 6000 projections with a pixel size of 21.80 mm. The total exposure time was 0.1 s (four accumulated images of 25 ms). For both sets of experiments, the centre of rotation was shifted near the edge of the field of view, almost doubling the size of reconstructed slices, keeping a margin ranging from 10% to 20% to ensure an overlap between projections 180 ̊ apart. Given the limited vertical size of the X-ray beam (ca. 7.5 mm), the full acquisition of a sample required several scans, moving various blocks of the specimen by 50% of the vertical field of view between each scan. The significant overlap was used to stitch radiographs vertically before tomo- graphic reconstruction. As the PCO.edge 5.5 produces a vertically banding noise, each image was de-noised: first, a 1D high-pass median filter with a width of 5 pixels was applied horizontally; sec- ond, a three passes 1D vertical median filter with a width corresponding to 50% of the vertical size of the image. The overlapping part of two consecutive scans required a registration: the horizontal alignment was based on the position of the centre of rotation, while the vertical alignment was eval- uated based on the mean error around the predicted value. Computation of the overlapping part was handled in two parts. The low frequencies (based on a low-pass median filter of a few pixels in width) were obtained using a weighted average, based on the vertical intensity profile of the beam. High frequencies (HFs) were handled to diminish the presence of strong ring artefacts in recon- structed slices: first, a blurred averaged of both HF images was generated; then a final image was generated, selecting pixels from both HF images that were less divergent from the blurred averaged image. Tomographic reconstruction was done using PyHST2 (Mirone et al., 2014) using the single dis- tance phase retrieval approach (Paganin et al., 2002). The d/b parameter (indicating the nature of the material for single-phase material) was set to reduce the noise while avoiding blurring of dense metallic inclusions. To reduce the impact of dense inclusions in the data, we performed a normaliza- tion of artifactual grey-level gradients and metallic inclusion correction (Cau et al., 2017). Remaining processing included modification of the bit depth from 32 to 16 bits, using the 0.001% minimum and maximum exclusion values of the 3D histogram generated by PyHST2; ring correction (Lyckegaard et al., 2011); and cropping the volume. Finally, a 2 􏰁 2 􏰁 2 binning was applied to increase the signal-noise-ratio and reduce the size of the data for segmentation.
Description attachment
None
Reference attachment
None

STEP 2: IMAGE PROCESSING

Raw media (undeposited) was processed to create derived Media 000668788: Skull Block [CTImageSeries] [Synchro] (this media).

Processing Details Field Definitions

Creator
Vincent Fernandez
Event date
--
Software
--
Description
Specimen AM 4766 was imaged on the ID17 beamline of The European Synchrotron (ESRF, Greno- ble, France). The experiment consisted of two parts: (1) imaging the whole of each block and (2) re- imaging specific regions of interest at higher resolution (i.e., the sternal region where anatomy is obscured by matrix and larger parts of the skeleton). The beamline was setup for propagation phase-contrast synchrotron X-ray micro-computed tomography: a monochromatic beam of 160 keV (Laue double bent Si 111), a sample-detector distance of 11 m and an indirect detector comprising a 2 mm LuAG scintillator, a set of lenses with a magnification of ~0.3􏰁, and a visible light detector (CCD or sCMOS). For the first set of experiments, we used a FReLoN 2k camera (ESRF), recording 4998 radiographs over a 360 ̊ rotation of the sample with a pixel size of 46.95 mm. Each radiograph consisted of five accumulated images, each with an exposure time of 40 ms, resulting in a total expo- sure time of 0.2 s per recorded radiograph. For the second part of the experiment, we used a PCO. edge 5.5 sCMOS with camera link (PCO, Kelheim, Germany), recorded 6000 projections with a pixel size of 21.80 mm. The total exposure time was 0.1 s (four accumulated images of 25 ms). For both sets of experiments, the centre of rotation was shifted near the edge of the field of view, almost doubling the size of reconstructed slices, keeping a margin ranging from 10% to 20% to ensure an overlap between projections 180 ̊ apart. Given the limited vertical size of the X-ray beam (ca. 7.5 mm), the full acquisition of a sample required several scans, moving various blocks of the specimen by 50% of the vertical field of view between each scan. The significant overlap was used to stitch radiographs vertically before tomo- graphic reconstruction. As the PCO.edge 5.5 produces a vertically banding noise, each image was de-noised: first, a 1D high-pass median filter with a width of 5 pixels was applied horizontally; sec- ond, a three passes 1D vertical median filter with a width corresponding to 50% of the vertical size of the image. The overlapping part of two consecutive scans required a registration: the horizontal alignment was based on the position of the centre of rotation, while the vertical alignment was eval- uated based on the mean error around the predicted value. Computation of the overlapping part was handled in two parts. The low frequencies (based on a low-pass median filter of a few pixels in width) were obtained using a weighted average, based on the vertical intensity profile of the beam. High frequencies (HFs) were handled to diminish the presence of strong ring artefacts in recon- structed slices: first, a blurred averaged of both HF images was generated; then a final image was generated, selecting pixels from both HF images that were less divergent from the blurred averaged image. Tomographic reconstruction was done using PyHST2 (Mirone et al., 2014) using the single dis- tance phase retrieval approach (Paganin et al., 2002). The d/b parameter (indicating the nature of the material for single-phase material) was set to reduce the noise while avoiding blurring of dense metallic inclusions. To reduce the impact of dense inclusions in the data, we performed a normaliza- tion of artifactual grey-level gradients and metallic inclusion correction (Cau et al., 2017). Remaining processing included modification of the bit depth from 32 to 16 bits, using the 0.001% minimum and maximum exclusion values of the 3D histogram generated by PyHST2; ring correction (Lyckegaard et al., 2011); and cropping the volume. Finally, a 2 􏰁 2 􏰁 2 binning was applied to increase the signal-noise-ratio and reduce the size of the data for segmentation.
Description attachment
None

Media produced by this event on MorphoSource

Media 000668788: Skull Block [CTImageSeries] [Synchro] (this media)