Computational protocol: Collagen fibers mediate MRI-detected water diffusion and anisotropy in breast cancers

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Protocol publication

[…] Samples fixed for 24 hours in 4% paraformaldehyde (PFA), were washed with phosphate buffered saline for 72 hours, and placed in a 10 mm NMR tube immersed in Fomblin perfluoro polyether solution (Solvay Sollexis). MRI was performed on a vertical 11.7 T Bruker Avance NMR spectrometer (Bruker Biospin, Billerica, MA, USA) equipped with micro-imaging accessories. A Micro 2.5 gradient set capable of maximum 1500 mT/m gradient strength with a 10 mm birdcage volume coil was used. High-resolution T2-weighted MRI, and DTI of the samples were performed in 3D with an isotropic resolution of 62.5 × 62.5 × 62.5 μm3. DTI was performed using a modified 3D diffusion-weighted gradient and spin echo (DW-GRASE) sequence with the following parameters: TE/TR = 36/1500 ms, 4 signal averages, two non–diffusion-weighted images and six diffusion directions, b = 2100 s/mm2, field of view (FOV) = 8 × 8 × 9 mm3, a matrix size of 128 × 128 × 150. For the ex vivo studies, DT images were acquired at high resolution to compare the DTI data to the high resolution microscopy and histopathology datasets. These high resolution scans took ~15 hours, and therefore had to be limited to six diffusion directions.Average diffusion-weighted (aDW) images and maps of ADC and FA were calculated using DTI Studio image processing software for both in vivo and ex vivo DTI data. Both in vivo and ex vivo experiments were performed at 37°C. The specimen temperature was maintained by an integrated temperature control system that monitored and maintained the bore temperature with warm air. […]

Pipeline specifications

Software tools GRASE, MRI Studio
Applications Miscellaneous, Magnetic resonance imaging
Organisms Homo sapiens
Diseases Breast Neoplasms, Neoplasms