For each electron tomography analysis, serial tomograms were compiled as a single TIFF file and analyzed using Avizo 3D Software (v. 2021.1.; Thermo Fisher Scientific). The structure of interest (e.g., LD, mitochondria, ER.) was carefully manually traced on each virtual slice using a Wacom graphic tablet and then reconstructed in three dimensions, with rendering generated using unconstrained smoothing parameters. The surfaces of adhesion/contact sites and mitochondria were measured using the Surface Area Volume module. Movies were generated using Avizo 3D Software (v. 2021.3, Thermo Fisher Scientific) and then edited with the Microsoft Photos application (v. 2022.30060.30007.0; Microsoft).
Avizo 3d software
Manufactured by Thermo Fisher Scientific
Avizo 3D Software is a high-performance data visualization and analysis tool designed for scientific and industrial applications. It provides advanced capabilities for processing, analyzing, and visualizing 3D data from a variety of sources, including microscopy, medical imaging, and industrial scanning.
Automatically generated - may contain errors
7 protocols using avizo 3d software
1
3D Reconstruction of Cellular Structures
2
3D Reconstruction of Cellular Structures
3
X-ray CT Imaging and Analysis of Savonnières Rock Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The Savonnières rock samples were x-ray CT imaged using a Siemens scanner SOMATOM Definition AS at an energy of 140 kV and current of 500 mA. X-ray CT transversal images were acquired with the best field of view capable to achieve a voxel size of 0.1 × 0.1 × 0.1 mm. Avizo 3D software from Thermofisher and Osirix MD software from Pixmeo were used to process the X-ray images and generate 2D and 3D views to observe the samples' inner structure before and after testing. After applying non-local mean filtering to remove some noise from the images, a single threshold on the CT histogram with a CT number less than 500 HU was used to segment the pores/open structures.
A low pass filter was applied to the segmented image to remove small pores and artefacts on the images. In order to only see generated fractures/faults from the geomechanical experiment, an island removal of 50 pixels (i.e., ≤ 5 mm object size) was applied to remove most pores in Savonnieres sample (pore diameter « 5 mm diameter) and keep only the main big size open structures (i.e., >5 mm) like faults [51 ]. A volume rendering of the segmented images was finally produced on Osirix MD software to visualise the whole structures and match the orientation of the visible structures on the surface of the plug.
A low pass filter was applied to the segmented image to remove small pores and artefacts on the images. In order to only see generated fractures/faults from the geomechanical experiment, an island removal of 50 pixels (i.e., ≤ 5 mm object size) was applied to remove most pores in Savonnieres sample (pore diameter « 5 mm diameter) and keep only the main big size open structures (i.e., >5 mm) like faults [51 ]. A volume rendering of the segmented images was finally produced on Osirix MD software to visualise the whole structures and match the orientation of the visible structures on the surface of the plug.
4
Shark Specimen Staining and Imaging
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Shark samples previously fixed in 4% paraformaldehyde (PFA) and dehydrated for freezer storage were stained with 1% I2 dissolved in ethanol according to Metscher65 (link). X-ray computed tomography scans were done using a Zeiss Xradia 520 Versa system. Images were generated using Avizo 3D software (ThermoFisher Scientific).
5
Quantifying Mitochondrial Ultrastructure
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The image analysis was carried out using Avizo 3D software (FEI). First, the mitochondrial OM of the tomographic reconstruction was defined manually. The COX-positive versus -negative densities within the OM were segmented automatically by a threshold method and the volumes of COX-positive versus -negative densities were calculated. The COX-positive lamellar versus reticular structures were defined by the volume larger or smaller than 1 × 106 nm3, respectively. The cristae in contact with the IBM were defined by the cristae within the distance of 50 nm from the OM. By manual inspection, cristae connecting to the other cristae within the distance of 50 nm from the OM were also counted as being in contact with the IBM.
6
Serial Sectioning and Electron Tomography
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Serial sections with thickness of 200 nm or 250 nm were prepared and collected on copper slot grids (2 × 0.5 mm oval slots) with carbon supports, on which overlaid with 10 nm fiducial gold pretreated with BSA. The grids were stained with Reynold’s lead citrate before the second layer of fiducial gold was applied. The specimens were imaged with FEI Tecnai TEM operating at 200 kV and the micrographs were recorded with a Gatan UltraScan 1000 CCD at 0.87 nm/pixel (9,600x). Tilt series from −60° to +60° with 2° increments were acquired using Xplore3DTM (FEI). Double tilt series were collected using a double tilt holder (Model 2040 Dual-Axis Tomography Holder, Fischione). Serial tomograms were reconstructed, joined using IMOD, and segmented using Avizo 3D software (FEI).
7
Cryo-electron Tomography of Cellular Ultrastructure
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The procedure was performed as previously described (Jiang et al., 2017a , b (link)). Serial sections with a thickness of 200 nm were prepared and collected on copper slot grids (2 × 0.5 mm oval slots) with carbon supports, which were overlaid with 10 nm fiducial gold that was pretreated with BSA. The grids were stained with Reynold’s lead citrate before the second layer of fiducial gold was applied. The specimens were imaged with an FEI Tecnai TEM operating at 200 kV. The micrographs were recorded with a Gatan UltraScan 1000 CCD at 0.87 nm/pixel (9600×). Tilt series from –60° to +60° with 2° increments were acquired at 10 μm defocus using Leginon automatic data collection software (Suloway et al., 2009 ). Double tilt series were collected using a double tilt holder (Model 2040 Dual-Axis Tomography Holder; Fischione). Serial tomograms were reconstructed, joined using IMOD, and segmented using Avizo 3D software (FEI).
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!