Computational protocol: Brain atlas of the Mongolian gerbil (Meriones unguiculatus) in CT/MRI-aided stereotaxic coordinates

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Protocol publication

[…] Animals were anesthetized with isoflurane (1.0–1.5 % in 1:1 O2:N2 volume ratio) and fixed with bite bars in a head-holder to reduce motion artifacts. MR scans were performed on a Bruker Biospec 47/20 scanner (Bruker Biospin GmbH, Rheinstetten, Germany) at 4.7 T (free bore of 20 cm) equipped with a BGA 09 (400 mT/m) gradient system. A 35 mm Litzcage small animal imaging system (DotyScientific Inc., Colombus, SC, USA) was used for radio frequency (RF) excitation and signal reception. Two days before MRI measurements, animals were injected subcutaneously with an aqueous solution containing 1 μmol/g MnCl2 (manganese enhanced MRI: ME-MRI). A data set of T1-weighted images was obtained using a 3D MDEFT (modified driven equilibrium Fourier transform) pulse sequence with the following parameters: repetition time 13.6 ms; echo time 4.3 ms; flip angle 20°; field of view 30 × 30 mm2; matrix 256 × 256 (yielding a nominal in plane resolution of 117 × 117 µm2); standard frontal orientation; slice thickness 350 µm; 20 averages. Images were reconstructed using Bruker ParaVision 4.0 (Bruker Biospin GmbH, Rheinstetten, Germany) and exported as raw images as well as in DICOM format. The open source program AMIDE (amide.exe 1.0.4, ©Andreas Loening, http://amide.sourceforge.net/) was used to align CT and MR scans and to extract images shown in the atlas. [...] For each 350 µm thick slice of the atlas MR series a corresponding Nissl-stained section of the atlas series was selected and grouped with the adjacent myelin-stained section to represent one of the 62 rostro-caudal levels (Fig. ). Usually, every forth Nissl-stained section fitted best to the subsequent MR slice, which corresponded to a distance of 320 µm between the matching Nissl-stained sections. The 30 µm difference between the MR slices and the Nissl-stained sections can be explained by the shrinkage of the atlas brain due to histological processing, mainly fixation. This shrinkage is in the range of 8–10 % generally observed for cryo-protected frozen-cut brains with PFA fixation (4 %). Contrast and brightness of the images of the sections were corrected with Photoshop (CS6, Adobe Systems, San Jose, CA, USA), and distortions due to histological processing were compensated by slightly transforming the sections to optimize the congruency of anatomical structures between histological sections and MR images. Images were arranged in the atlas coordinate frame using CorelDraw graphics suite version X6 or X7 (Corel Corporation, Ottawa, ON, Canada). MR and CT images were adjusted according to the definition of the atlas coordinate system in 62 plates and reflect the in vivo orientation of the brain and skull. The images of cell- and myelin-stained sections were inserted in line with the corresponding MR image. The anterior–posterior coordinates of the plates are indicated relative to bregma, lambda, interaural line and the occipital crest. All outlines were drawn in CorelDraw on the base of the Nissl-stained section of each atlas plate. The structural boundaries seen in the corresponding myelin-stained section generally correlate well with these outlines. […]

Pipeline specifications

Software tools ParaVision, CorelDraw
Applications Miscellaneous, Magnetic resonance imaging
Organisms Meriones unguiculatus, Dipturus trachyderma