Dataset Information

Comparison of Transparency and Shrinkage During Clearing of Insect Brains Using Media With Tunable Refractive Index.

ABSTRACT: Improvement of imaging quality has the potential to visualize previously unseen building blocks of the brain and is therefore one of the great challenges in neuroscience. Rapid development of new tissue clearing techniques in recent years have attempted to solve imaging compromises in thick brain samples, particularly for high resolution optical microscopy, where the clearing medium needs to match the high refractive index of the objective immersion medium. These problems are exacerbated in insect tissue, where numerous (initially air-filled) tracheal tubes branching throughout the brain increase the scattering of light. To date, surprisingly few studies have systematically quantified the benefits of such clearing methods using objective transparency and tissue shrinkage measurements. In this study we compare a traditional and widely used insect clearing medium, methyl salicylate combined with permanent mounting in Permount ("MS/P") with several more recently applied clearing media that offer tunable refractive index (n): 2,2'-thiodiethanol (TDE), "SeeDB2" (in variants SeeDB2S and SeeDB2G matched to oil and glycerol immersion, n = 1.52 and 1.47, respectively) and Rapiclear (also with n = 1.52 and 1.47). We measured transparency and tissue shrinkage by comparing freshly dissected brains with cleared brains from dipteran flies, with or without addition of vacuum or ethanol pre-treatments (dehydration and rehydration) to evacuate air from the tracheal system. The results show that ethanol pre-treatment is very effective for improving transparency, regardless of the subsequent clearing medium, while vacuum treatment offers little measurable benefit. Ethanol pre-treated SeeDB2G and Rapiclear brains show much less shrinkage than using the traditional MS/P method. Furthermore, at lower refractive index, closer to that of glycerol immersion, these recently developed media offer outstanding transparency compared to TDE and MS/P. Rapiclear protocols were less laborious compared to SeeDB2, but both offer sufficient transparency and refractive index tunability to permit super-resolution imaging of local volumes in whole mount brains from large insects, and even light-sheet microscopy. Although long-term permanency of Rapiclear stored samples remains to be established, our samples still showed good preservation of fluorescence after storage for more than a year at room temperature.

SUBMITTER: Bekkouche BMB

PROVIDER: S-EPMC7714936 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Comparison of Transparency and Shrinkage During Clearing of Insect Brains Using Media With Tunable Refractive Index.

Bekkouche Bo M B BMB Fritz Helena K M HKM Rigosi Elisa E O'Carroll David C DC

Frontiers in neuroanatomy 20201120

Improvement of imaging quality has the potential to visualize previously unseen building blocks of the brain and is therefore one of the great challenges in neuroscience. Rapid development of new tissue clearing techniques in recent years have attempted to solve imaging compromises in thick brain samples, particularly for high resolution optical microscopy, where the clearing medium needs to match the high refractive index of the objective immersion medium. These problems are exacerbated in inse ...[more]

PMID: 33328907

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Project description:Achieving accurate optical-CT 3D dosimetry without the use of viscous refractive index (RI) matching fluids would greatly increase convenience.Software has been developed to simulate optical-CT 3D dosimetry for a range of scanning configurations including parallel-beam, point, and converging light sources. For each configuration the efficacy of three refractive media was investigated: air, water, a fluid closely matched to PRESAGE(®), and perfect matching (RI = 1.00, 1.33, 1.49, and 1.501 respectively). Reconstructions were performed using both filtered backprojection (FBP) and algebraic reconstruction technique (ART). The efficacy of the three configurations and the two algorithms was evaluated by calculating the usable radius (i.e., the outermost radius where data were accurate to within 2%), and gamma (Γ) analysis. This definition recognizes that for optical-CT imaging, errors are greatest near the edge of the dosimeter, where refraction can be most pronounced. Simulations were performed on three types of dose distribution: uniform, volumetric modulated arc therapy (VMAT), and brachytherapy (Cs-137).For a uniformly irradiated dosimeter the usable radius achieved with filtered backprojection was 68% for water-matching and 31% for dry-scanning in air. Algebraic reconstruction gave usable radii of 99% for both water and air (dry-scanning), indicating greater recovery of useful data for the uniform distribution. FBP and ART performed equally well for a VMAT dose distribution where less dose is delivered near the edge of the dosimeter. In this case, the usable radius was 86% and 53% for scanning in water and air, respectively. For brachytherapy, the usable radius was 99% and 98% for scanning in water and air, respectively using FBP, and a major decrease was seen with ART. Point source geometry provided 1%-2% larger usable radii than parallel geometry. Converging geometry recovered less usable dosimetry data (up to 10% reduced usable radii) than point and parallel geometries. A further disadvantage of converging geometry was an increased requirement on detector size by up to 18°.For applications where dose information is not required in the periphery of the dosimeter, some dry and low-viscous matching configurations may be feasible. For all three dose distributions (uniform, VMAT, brachytherapy) the point source geometry produced slightly more favorable results (an extra 1%-2% usable radii) than parallel and converging. When dosimetry is required on the periphery, best results were obtained using close refractive matching and ART. A concern for water or dry-scanning is the increase in required detector size, introducing potential cost penalties for manufacturing.

Dataset Information

Comparison of Transparency and Shrinkage During Clearing of Insect Brains Using Media With Tunable Refractive Index.

Publications

Comparison of Transparency and Shrinkage During Clearing of Insect Brains Using Media With Tunable Refractive Index.

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