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45 protocols using fomblin

1

Volumetric Analysis of Right Brain Hemisphere

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The volume of the right brain hemisphere, white matter, and grey matter were measured by MRI as previously described (Henriksen et al., 2022a (link)). Briefly, the entire right hemisphere was immersed in 4% paraformaldehyde in phosphate buffered saline for 24 h at 4°C (PBS; 0.1 M, pH 7.4), rehydrated with PBS for 24 h at 4°C and washed twice with Fomblin (perfluoro-polyether; Solvay, Princeton, New Jersey, USA) to remove the excess fluid and resubmerged in clean Fomblin prior to scanning. It was confirmed that there was no surrounding fluid signal on the surface of each brain before high-resolution imaging. Data was acquired with a 9.4 Tesla preclinical scanner (Bruker BioSpin, Ettlingen, Germany) equipped with a 240 mT/m gradient coil (BGA-12S, Bruker) and using an 86-mm inner diameter transmit-receive volume coil. The imaging protocol used a 3D gradient-spoiled steady state free precession, and the parameters were set to: repetition time = 4.6 ms, echo time = 2.3 ms, number of signals averaged = 10, flip angle = 25°, field of view = 60 mm × 38.4 mm × 25.6 mm, matrix = 300 × 192 × 128, image resolution = 200 μm isotropic, acquisition time = 20 min. The images were bias-field corrected, and segmented as previously described (Henriksen et al., 2022a (link)). The volume of white and grey matter was normalized to the total volume of the brain hemisphere.
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2

Ex Vivo Diffusion MRI of Traumatic Brain Injury

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Specimen brains were excised 11 weeks after injury and prepared for ex vivo imaging. The 11 week time point was selected to coincide with a prior study examining DTI parameter changes throughout the spinal cord. 8 Animals were euthanized with an IP injection of sodium pentobarbital (100 mg/kg body weight) and perfused through the heart with 300 mL of saline buffer followed by 600 mL of 10% formalin. The brains were excised and postfixed in a 10% formalin solution until the day of scanning. The brains were immersed in a susceptibility-matching fluid (Fomblin; Solvay Solexis, Inc, West Deptford, NJ) and placed in an inductively coupled 20 mm diameter loop gap radiofrequency coil. Specimens were positioned in a 9.4T Bruker BioSpec 94/30 USR Spectroscopy Imaging System (Bruker BioSpin; Billerica, MA). A multiecho (eight echos) spin-echo sequence was used to acquire 12 diffusion weighted images (DWIs) with a b-value of 2000 s/mm 2 and two images with a b-value of 0 s/mm 2 . A b-value of 2000 s/mm 2 was used for high diffusion contrast. An echo time (TE) of 25 ms and a repetition time (TR) of 3000 ms was used when acquiring scans that had a field of view (FOV) size of 20 mm by 20 mm, acquisition matrix of 128 3 128, and 0.75-mm-thick slices that were contiguously arranged for 30 slices.
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3

Postmortem MRI of Brain Tissue

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The postmortem CNS tissue donated to the lab for scientific research was first fixed in 10% formalin for two weeks and then stored in 1% formalin to avoid over-fixation. High-resolution, whole hemisphere MRI was performed on the donated tissue to identify abnormal regions, as described elsewhere. (Absinta et al., 2014 (link)) Briefly, images were placed in a postmortem imaging container filled with Fomblin (Solvay Solexis, West Deptford, NJ), which closely fit into a 32-channel head coil (NOVA medical, Wilmington MA). Images were acquired on a Magnetom 7T MRI system (Siemens, Malvern, PA) equipped with a circular-polarized transmit/32-channel receive coil. Imaging included a T2*-weighted sequence (3D gradient-echo sequence, TR = 60 ms, multiple TEs of 6.09, 15.99, 25.89, 35.79 ms, FA = 10°, 4 averages, 88 slices, 0.42 mm isotropic resolution, acquisition time = 2.25 h per 3D slab).
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4

Postmortem MRI of Brain Tissue

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The postmortem CNS tissue donated to the lab for scientific research was first fixed in 10% formalin for two weeks and then stored in 1% formalin to avoid over-fixation. High-resolution, whole hemisphere MRI was performed on the donated tissue to identify abnormal regions, as described elsewhere. (Absinta et al., 2014 (link)) Briefly, images were placed in a postmortem imaging container filled with Fomblin (Solvay Solexis, West Deptford, NJ), which closely fit into a 32-channel head coil (NOVA medical, Wilmington MA). Images were acquired on a Magnetom 7T MRI system (Siemens, Malvern, PA) equipped with a circular-polarized transmit/32-channel receive coil. Imaging included a T2*-weighted sequence (3D gradient-echo sequence, TR = 60 ms, multiple TEs of 6.09, 15.99, 25.89, 35.79 ms, FA = 10°, 4 averages, 88 slices, 0.42 mm isotropic resolution, acquisition time = 2.25 h per 3D slab).
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5

Nerve and Limb Imaging Using MRI

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After 24 hours of postfixation, excised nerves were placed in PBS plus 2 mM Gd-diethylene triamine pentaacetic acid (DTPA) (Magnevist, Bayer HealthCare) at 4°C for at least 24 hours before imaging. For imaging, excised nerves were trimmed to approximately 1 cm in length (with the injury site centered) and placed in glass capillary tubes (2-mm outer diameter) filled with a perfluropolyether liquid (Fomblin, Solvay Solexis) for susceptibility matching, preventing tissue dehydration, and a signal-free background. For higher throughput, 6 excised sciatic nerves in a hexagonal arrangement were imaged simultaneously. Hindlimb samples were postfixed for 1 week, followed by at least 1 week of washing in PBS plus 2 mM Gd-DTPA before imaging. For imaging, hind limbs were placed in MR-compatible tubes filled with perfluoropolyether liquid.
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6

Quantifying Myocardial Oxygenation via MRI

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ADN (5 mg kg−1) was injected intravenously into C57BL/6 mice and allowed to circulate. After 4 h, mice were killed and the hearts were perfused with PBS, bisected along the short axis, embedded in optimal cutting temperature compound (Tissue-Tek, Sakura) and stored at −80 °C. At the time of imaging, the heart tissue was thawed, placed in fomblin (Solvay), and MRI was performed on a 9.4 Tesla horizontal bore magnet (Biospec, Bruker). Transverse relaxivity (R2*) maps were generated from multi-echo gradient echo images, acquired in the short axis of the left ventricle, with the following settings: repetition time (TR) 500 ms, 14 echo times (TE) beginning at 1.784 ms with an increment of 1.25 ms, four averages, field of view 28.8 mm × 28.8 mm, matrix dimension 192 × 192, spatial resolution 0.15 mm × 0.15 mm, slice thickness 0.5 mm, flip angle 10°.
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7

Ex Vivo MRI Imaging of Tissue Samples

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Ex vivo imaging sessions were performed for the WT mice to better correlate measures to the IHC data. After in vivo imaging and transcardial perfusions, one leg sample was immersed in 4% PFA overnight at 4°C, and washed similarly to the immunohistochemistry samples in PBS twice for 30 minutes each. Following the wash, the ex vivo samples were transferred to a fresh PBS for 2 days for full rehydration at 4°C. Before ex vivo imaging, the set of samples were allowed to get to room temperature and situated in a holder filled with Fomblin (Solvay Solexis Inc, Thorofare, NJ), which serves as a hydrophobic sealant to contain the water within the samples during the long imaging sessions. Four samples were scanned together in a container using the same 7T Biospec micro-MRI system. The same scan protocol used for the in vivo MRI scan was used for the ex vivo MRI scans. The ex vivo scans were conducted with the all animals used for the in vivo MRI study. All ex vivo scans were performed at room temperature (20±2°C).
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8

Post-mortem MRI of Whole Brain

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At the conclusion of the experiment, animals were transcardially perfused with cold 4% paraformaldehyde (PFA), and the whole brain was removed and placed in 10% neutral buffered formalin. Brains were placed in a plastic tube filled with nonmagnetic oil (Fomblin; Solvay, Brussels, Belgium), and postmortem MRI was obtained in the same magnet using a 38-mm inner-diameter birdcage volume RF coil. For each animal, whole brain 3D T2*-weighted MGRE (multi gradient echo; nominal resolution=0.1 mm isotropic; TR=57 ms; shortest TE=3.6 ms; echo spacing=4 ms; number of echoes=10; FA=90 deg; AT=1.1 hour; number of excitations=8) and 2D T2-weighted RARE (nominal in-plane resolution=0.1 mm × 0.1 mm; ST=0.3 mm; TR=1200 ms; TE=12 ms; AT time=50 min; number of excitations=8) were acquired.
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9

Nerve Excision and Repair Imaging

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After nerve excision, reverse autografts were incubated in 4% glutaraldehyde/0.5% paraformaldehyde in phosphate-buffered saline (PBS) at 4°C and nerves repaired with a UBM conduit were incubated in 4% glutaraldehyde/2% paraformaldehyde in PBS at 4°C for better penetration of the conduit material. After a minimum of 24 hours of postfixation, excised nerves were placed in PBS + 2 mM gadolinium diethylene triamine pentaacetic acid (Magnevist, Bayer HealthCare, Wayne, NJ) at 4°C for at least 24 hours before imaging. For imaging, excised nerves were placed in glass capillary tubes (3-mm outer diameter) filled with a perfluropolyether liquid (Fomblin, Solvay Solexis, Thorofare, NJ) for susceptibility matching, preventing tissue dehydration, and a signal-free background. For higher throughput, 6 nerves in a hexagonal arrangement were imaged simultaneously.
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10

High-field ex vivo brain MRI

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All scanning was performed on a 14 T vertical Bruker Micro imaging system with a 30 mm RF coil. The ex vivo brains were rehydrated in phosphate-buffered saline for at least 3 days before imaging and immersed in perfluoro polyether (FOMBLIN®, Solvay Specialty Polymers Italy SpA) to avoid magnetic susceptibility artifacts during MRI scanning. Diffusion weighted image (DWI) was achieved using a three-dimensional echo planar imaging (EPI) sequence with eight segments: TE/TR = 31/800 ms, b = 3,800 s/mm2, 32 gradient directions, δ/Δ = 3/18 ms, 0.16 × 0.16 × 0.16 mm3 voxel size, and two acquisitions at b = 0 s/mm2. Here, the b values were chosen to induce similar diffusion signal attenuation as conventional DTI in vivo (b around 1,000 s/mm2) as the diffusivity in ex vivo brain is around 3–4 times smaller than that in in vivo brain. Similar b values were also used by other groups for ex vivo studies (Irfanoglu et al., 2016 (link); Haber et al., 2017 (link)). DWIs with the opposite phase-encoded directions were acquired at b = 0 s/mm2 for geometric distortion correction for EPI. The total time for DWI acquisitions was 7 h 20 min 58 s. T2-weighted images were obtained using a three-dimensional multislice multi-echo sequence (MSME) with the same spatial dimensions as DWIs: TE/TR = 4/1,000 ms and 32 echoes.
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