Media 000623999: Hearing Apparatus
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Type
Mesh
Modality
X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
Managed by
Media 000623999: Hearing Apparatus
Open Download
Type
Mesh
Modality
X-Ray Computed Tomography (CT/microCT)
Media represents biological specimen
Managed by
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GENERAL DETAILS Field Definitions
Media ID
000623999
Media type
Mesh
Object element or part
Hearing apparatus
Object represented
Object taxonomy
Danionella cerebrum
Object organization
Side
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Orientation
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Short description
Micro CT segmentation of adult male Danionella cerebrum
Full description
Paper: "The mechanism for directional hearing in fish" (https://www.nature.com/articles/s41586-024-07507-9).
The raw data and full resolution meshgrid data is available at
https://gin.g-node.org/danionella/Veith_et_al_2024/src/master/microCT
Method:
A 12-month-old male wild-type Danionella c. was euthanized by ice shock and fixed with 4% paraformaldehyde in phosphate-buffered saline (PBS) at 4 °C overnight. The next day, the fish was washed for 15 minutes in PBS before being stained with 5% phosphomolybdic acid (Sigma Aldrich) solution in PBS at 4 °C overnight. After staining, the fish was washed in PBS for 15 minutes before embedding in 1% PBS buffered agarose inside a cryo tube. The micro-CT scan was performed at the ANATOMIX beamline at SOLEIL synchrotron by XPLORAYTION GmbH. The sample was placed into a 40 keV polychromatic (white) X-ray beam. A scan consisted of 3200 projections collected at ~10x optical magnification by a digital camera (Orca Flash 4.0 V2) with a sensor pixel size of 6.5 µm at 150 ms exposure time, yielding an effective pixel size of 0.6485 µm. The registered data were binned to 1.2970 µm voxel size. Key structures of the hearing apparatus were manually segmented. To this end, planes were hand-labeled using 3D Slicer (v5.6, slicer.org) and then interpolated using Biomedisa (v23). FIJI ImageJ (v1.5) was used to convert between different file types. The segments were turned into mesh grids and loaded into Blender for cleaning and rendering.
Creator
--
Date created
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Date uploaded
April 26, 2024
FILE OBJECT DETAILS Field Definitions
File name
Danionella_cerebrum_adult_male_Veith_et_al.glb
File format(s)
gLTF
File size
19.1 MB
Points
676433
Polygons
469212
Map type
--
UV coordinates
False
Vertex color
False
Bounding box dimensions
43.146, 21.635, 22.574
Centroid coordinates
6.613, -3.627, -0.493 (Bounding Box)
Units of point coordinates
--
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
Custom ANATOMIX Beamline, Synchrotron SOLEIL (Synchrotron SOLEIL)
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 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
Not assigned
External identifier
--
External media URL
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IMAGE ACQUISITION AND PROCESSING IN DETAIL
STEP 1: IMAGE ACQUISITION
Physical object
CUB:Fish
was imaged to create
undeposited raw media.
IMAGING DETAILS Field Definitions
Modality
X-Ray Computed Tomography (CT/microCT)
Device
Device facility
Synchrotron SOLEIL (Synchrotron SOLEIL)
Creator
--
Event date
--
Software
--
Description
A 12-month-old male wild-type Danionella c. was euthanized by ice shock and fixed with 4% paraformaldehyde in phosphate-buffered saline (PBS) at 4 °C overnight. The next day, the fish was washed for 15 minutes in PBS before being stained with 5% phosphomolybdic acid (Sigma Aldrich) solution in PBS at 4 °C overnight. After staining, the fish was washed in PBS for 15 minutes before embedding in 1% PBS buffered agarose inside a cryo tube. The micro-CT scan was performed at the ANATOMIX beamline at SOLEIL synchrotron by XPLORAYTION GmbH. The sample was placed into a 40 keV polychromatic (white) X-ray beam. A scan consisted of 3200 projections collected at ~10x optical magnification by a digital camera (Orca Flash 4.0 V2) with a sensor pixel size of 6.5 µm at 150 ms exposure time, yielding an effective pixel size of 0.6485 µm. The registered data were binned to 1.2970 µm voxel size. Key structures of the hearing apparatus were manually segmented. To this end, planes were hand-labeled using 3D Slicer (v5.6, slicer.org) and then interpolated using Biomedisa (v23). FIJI ImageJ (v1.5) was used to convert between different file types. The segments were turned into mesh grids and loaded into Blender for cleaning and rendering.
Raw data and full resolution segmentation meshgrids are deposited at https://gin.g-node.org/danionella/Veith_et_al_2024/src/master/microCT
The data deposited here constitutes downsampled meshgrids.
Description attachment
None
Reference attachment
None
Exposure time
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Flux normalization
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Pixel spacing calibration
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Shading correction
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Frame averaging
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Projections
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Voltage
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Surrounding material
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X-ray tube type
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Target type
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Detector pixels size X
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Source detector distance
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Target material
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Rotation number
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Phase contrast
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Optical magnification
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Acquisition type
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STEP 2: IMAGE PROCESSING
Raw media (undeposited)
was processed
to create
derived
Media 000623999: Hearing Apparatus [Mesh] [CT] (this media).
Processing Details Field Definitions
Creator
--
Event date
--
Software
--
Description
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Description attachment
None