This study was performed under the University of Utah Institutional Review Board approved protocol #11755. An existing data set was utilized for this study, and the methods for cadaver selection and the creation of DRR have been described previously.24 (link) These cadavers were screened for osteoarthritis and rotator cuff tears by direct visualization during dissection, and 3D CT reconstructions were evaluated by an orthopedic surgeon fellowship trained in shoulder and elbow surgery (TS). As many cadavers are advanced in age, cadavers were carefully screened for these pathologies, which are common in these age groups. Sixty-eight cadaver shoulders (25 pairs and 18 individual scapulae) were included. All cadavers underwent CT scans performed with a Siemens Sensation (Siemens Medical, Malvern, PA) CT scanner (130 kV, 512 × 512 matrix, 1.0 mm slice thickness, 0.75 pitch, 170-mAS current). These images were exported to DICOM (Digital Imaging and Communications in Medicine) format and semiautomatically segmented (Amira v5.4; Visage Imaging, San Diego, CA) and reconstructed into 3D surfaces, then used to create DRRs. The methodology for the creation of DRRs has been previously validated for reproducibility and accuracy.21 (link) This sample size was selected, as it was adequate for a similar prior study, and we did not perform an a priori power analysis.24 (link)
Amira v5
Manufactured by Visage Imaging
Sourced in Germany
Amira v5.4 is a software application designed for the visualization and analysis of 3D data. It provides a comprehensive suite of tools for handling and processing a wide range of data formats, including images, volumetric data, and mesh models.
Automatically generated - may contain errors
Lab products found in correlation
8 protocols using amira v5
1
3D Shoulder Anatomy Reconstruction
2
3D Shoulder Imaging and Reconstruction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
This study was performed under the University of Utah Institutional Review Board
approved protocol #11755. An existing data set was utilized for this study, and
the methods for cadaver selection and the creation of DRR have been described previously.24 (link)
These cadavers were screened for osteoarthritis and rotator cuff tears by
direct visualization during dissection, and 3D CT reconstructions were evaluated
by an orthopedic surgeon fellowship trained in shoulder and elbow surgery (TS).
As many cadavers are advanced in age, cadavers were carefully screened for these
pathologies, which are common in these age groups. Sixty-eight cadaver shoulders
(25 pairs and 18 individual scapulae) were included. All cadavers underwent CT
scans performed with a Siemens Sensation (Siemens Medical, Malvern, PA) CT
scanner (130 kV, 512 × 512 matrix, 1.0 mm slice thickness, 0.75 pitch, 170-mAS
current). These images were exported to DICOM (Digital Imaging and
Communications in Medicine) format and semiautomatically segmented (Amira v5.4;
Visage Imaging, San Diego, CA) and reconstructed into 3D surfaces, then used to
create DRRs. The methodology for the creation of DRRs has been previously
validated for reproducibility and accuracy.21 (link)
This sample size was selected, as it was adequate for a similar prior
study, and we did not perform an a priori power analysis.24 (link)
approved protocol #11755. An existing data set was utilized for this study, and
the methods for cadaver selection and the creation of DRR have been described previously.24 (link)
These cadavers were screened for osteoarthritis and rotator cuff tears by
direct visualization during dissection, and 3D CT reconstructions were evaluated
by an orthopedic surgeon fellowship trained in shoulder and elbow surgery (TS).
As many cadavers are advanced in age, cadavers were carefully screened for these
pathologies, which are common in these age groups. Sixty-eight cadaver shoulders
(25 pairs and 18 individual scapulae) were included. All cadavers underwent CT
scans performed with a Siemens Sensation (Siemens Medical, Malvern, PA) CT
scanner (130 kV, 512 × 512 matrix, 1.0 mm slice thickness, 0.75 pitch, 170-mAS
current). These images were exported to DICOM (Digital Imaging and
Communications in Medicine) format and semiautomatically segmented (Amira v5.4;
Visage Imaging, San Diego, CA) and reconstructed into 3D surfaces, then used to
create DRRs. The methodology for the creation of DRRs has been previously
validated for reproducibility and accuracy.21 (link)
This sample size was selected, as it was adequate for a similar prior
study, and we did not perform an a priori power analysis.24 (link)
3
Morphometric Analysis of Seadragon Species
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Morphometric measurements were taken of the holotype and three paratypes, and compared with scaled photographs from field observations of leafy (n=25) and common seadragons (n=20; for details, see electronic supplementary material, file S1). The descriptive morphology follows [4 ], and proportional measurements were taken as in reference [28 ].
Micro-computed tomography (μCT) of the holotype was conducted at the Cartilage Tissue Engineering laboratory at the University of California San Diego. The specimen was imaged in a Skyscan 1076 (Kontich, Belgium), wrapped in ethanol-soaked gauze, and positioned in a sealed LDPE container. Imaging was conducted at 36 μm isotropic voxel size, applying an electrical potential of 100 kVp and a current of 100 μA, with a 1.0 mm aluminium filter. A beam-hardening correction algorithm was applied during image reconstruction. The reconstructed file size was 1000×1000×5482 pixels (xyz).
DICOM stacks were processed and segmented in Amira v. 5.4 (Visage Imaging, Inc.), and visualized in Maya 2014 service pack 4 (Autodesk, Inc.). X-ray radiographs of all seadragon species were obtained at Scripps Institution of Oceanography.
Micro-computed tomography (μCT) of the holotype was conducted at the Cartilage Tissue Engineering laboratory at the University of California San Diego. The specimen was imaged in a Skyscan 1076 (Kontich, Belgium), wrapped in ethanol-soaked gauze, and positioned in a sealed LDPE container. Imaging was conducted at 36 μm isotropic voxel size, applying an electrical potential of 100 kVp and a current of 100 μA, with a 1.0 mm aluminium filter. A beam-hardening correction algorithm was applied during image reconstruction. The reconstructed file size was 1000×1000×5482 pixels (xyz).
DICOM stacks were processed and segmented in A
4
Cerebral Cortical Morphometry from MRI
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cerebral cortical volume, cortical surface area, fronto-occipital (FO)-length, and cerebral hemisphere width were measured on coronal (transaxial) MRIs at equal Z-axis intervals (156 μm) using SliceOmatic software v4.3 (TomoVision, Montreal, Canada) as previously described [49 (link), 50 (link)]. Measurement references for FO-length and cerebral width are shown in S1 Fig . The cerebral cortex was segmented semi-automatically based on MRI contrasts and was rendered in 3D using SliceOmatic software (see Fig 1A ). The 3D image was used to compute the mean cortical thickness throughout the cerebral hemisphere using Amira v5.2 (Visage Imaging, San Diego, CA, USA) as previously described [8 (link), 49 (link), 50 (link)].
5
3D Reconstruction of Velopharyngeal Airway
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The reconstruction process used to create the velopharyngeal airway models has been described previously (8) (link). Briefly, end-expiratory axial MRIs of the upper airway (nasal choanae to the larynx) were imported into 3-D data visualization software (Amira v5.2; Visage Imaging, CA), and the velopharyngeal mucosal surface (air-mucosa interface) was automatically segmented from the nasal choanae to the base of the uvula, thus creating a series of luminal contours representing the velopharyngeal airway mucosal surface. The luminal contours were exported into a nonuniform rational basis spline-based 3-D model and computer-aided design package (Rhinoceros v4; Robert McNeel and Associates, WA), smoothed, and the velopharyngeal mucosal surface reconstructed.
6
Embryonic Kidney Histology and 3D Reconstruction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Serial transverse sections (10 μm thickness) of whole embryos were digitalized with an Olympus virtual slide system (VS120-S5-J; Olympus Corp., Tokyo, Japan) for histological observations and 3-D reconstructions [22 ]. Sequential 2-D images at 25× magnification were digitally cropped around the metanephros. The metanephros, including the UCS, was segmented into serial digital sections. Three-dimensional images were computationally reconstructed and their morphology was analyzed using Amira v. 5.5.0 (Visage Imaging GmbH, Berlin, Germany). The total number of nephrons and those connected to the UCS were counted.
7
Metanephros Branching Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The longitudinal metanephros length (mm) and the volumes of the UCS and the whole metanephros (mm3) were calculated with Amira v. 5.5.0 (Visage Imaging GmbH, Berlin, Germany). The UCS volume was that of the segment between the zeroth- and fifth metanephros branching generations. The 3-D coordinates of all branching points were acquired using Amira 5.5.0 (Visage Imaging GmbH, Berlin, Germany). The coordinates were analyzed with Matlab v. R2017b (MathWorks, Inc., Natick, MA, USA) to calculate the generation of all branches. The following parameters were calculated according to each CS: (a) average UCS end-branching generation; (b) total amount of UCS end-branching; and (c) maximum UCS end-branching generation. The four lobes were defined as upper-polar, upper-interpolar, lower-interpolar, and lower-interpolar according to the second UCS branching generation. The polar lobe (PL) group included the upper- and lower-polar lobes whereas the interpolar lobe (IL) group included the upper- and lower-interpolar lobes. Deviations of the end-branching between the PL- and IL groups were statistically analyzed.
8
3D Reconstruction of Metanephros
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Histological sections of the metanephros were digitalized, and three-dimensional (3D) reconstructions were generated as described previously [12 (link)]. Briefly, serial transverse sections (thickness, 10 μm) of whole embryos were digitalized using an Olympus virtual slide system (VS120-S5-J, Olympus Corp., Tokyo, Japan) for histological observations and 3D reconstructions. Sequential two-dimensional (2D) images at 25× magnification were digitally cropped around the metanephros. The metanephros, including the UCS, was segmented into serial digital sections. 3D images and the centerline of the UCS were computationally reconstructed and analyzed using Amira v. 5.5.0 (Visage Imaging GmbH, Berlin, Germany).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!