Samples were scanned using Plan‐Apochromat 63×/1.32 Oil DIC objective at a resolution of 1,024 × 1,024 pixels with 8‐bit sampling in sequential scanning frame‐by‐frame mode. Single optical sections were acquired using identical acquisition settings, with the pinhole of 1 Airy Unit. Stacks of 8–29 optical sections yielded voxel dimensions between 100 and 300 nm for the X, Y and Z planes. 3D reconstructions were generated with Amira Software 2020.2 (Thermo Fisher Scientific). First, the surface area of the bassoon‐positive synaptic contacts was reconstructed using the Amira segmentation editor. Bassoon/PRK R1α‐positive contacts were defined by color‐coding the surface of PRK R1α cells found within 250 nm from bassoon‐positive varicosities. Subsequently, the surface of ‘250‐nm‐distant’ PRK R1α‐positive voxels was mapped onto Bassoon‐positive contact using the “surface distance” tool and plotted as a histogram.
Amira software 2020
Manufactured by Thermo Fisher Scientific
Amira Software 2020.2 is a comprehensive platform for 3D data visualization, analysis, and processing. It is designed to handle a wide range of data types, including microscopy, tomography, and clinical imaging data. The software provides tools for segmentation, quantification, and rendering, allowing users to extract meaningful insights from complex 3D datasets.
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Lab products found in correlation
2 protocols using amira software 2020
1
3D Reconstruction of Bassoon-Positive Synaptic Contacts
2
3D Reconstruction and Colocalization Analysis of Cell Interactions
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Samples were scanned using a Plan-Apochromat ×63/1.32 oil differential interference contrast objective at a resolution of 1024 × 1024 pixels with 8-bit sampling in sequential scanning frame-by-frame mode. Single optical sections were acquired using identical acquisition settings, with the pinhole of 1 Airy unit. Stacks of 8 to 29 optical sections yielded voxel dimensions between 100 and 400 nm for the x, y, and z planes. Three-dimensional reconstructions were generated with Amira Software 2020.2 (Thermo Fisher Scientific). First, the surface area of the CADM1+, CD8+, and/or CD68+ cells was reconstructed using the Amira segmentation editor. CADM1/CD8+ and/or CADM1/CD68+ contacts were defined by color-coding the surface of CD8+ and/or CD68+ cells found within 500 nm of CADM1+ soma. Subsequently, the surface of 500 nm distant CD8+ and/or CD68+ voxels was mapped onto CADM1+ cells using the surface-distance tool and plotted as a histogram. For 3D colocalization analysis, 3D imaging reconstructions were performed with Imaris software (version 9.8; Oxford Instruments) using the Imaris surface editor. Colocalization was analyzed with ImarisColoc plugins.
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