Mouse warp registry1/24/2024 Interpretation of brain-related data requires precise information about the anatomical location from which the data are derived. By having coordinates assigned to the experimental images, further analysis of the distribution of features extracted from the images is greatly facilitated. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of sectional images to reduce the amount of manual steps required. In this way, the spatial relationship between experimental image and atlas is defined, without introducing distortions in the original experimental images. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. A key feature in the tool is the capability to generate user defined cut planes through the reference atlas, matching the orientation of the cut plane of the sectional image data. Here we present QuickNII, a stand-alone software tool for semi-automated affine spatial registration of sectional image data to a 3D reference atlas coordinate framework. Overall, efficient tools for registration of large series of section images to reference atlases are currently not widely available. A major challenge in this regard is that microscopic sections often are cut with orientations deviating from the standard planes used in the reference atlases, resulting in inaccuracies and a need for tedious correction steps. However, anatomical location of observations made in microscopic sectional images from rodent brains is typically determined by comparison with 2D anatomical reference atlases. Modern high throughput brain wide profiling techniques for cells and their morphology, connectivity, and other properties, make the use of reference atlases with 3D coordinate frameworks essential. Iterative manual registration of sections is performed until a satisfactory result is reached across the series of images. Registration of more than one section to atlas (situation 3, red dashed line) results in repositioning of the other sections in the series relative to the reference atlas. (D) Section from A (grey) and atlas plate from C (blue) superimposed. The angle of orientation and the scaling (not shown) defined for the adjusted atlas plate is automatically propagated across the series, while distances among sections are automatically stretched or compressed. In the middle and bottom rows, the assumed position of the section shown as is indicated in situation 1 (solid line relative to sagittal and horizontal atlas diagrams, shown in the middle and lower rows, respectively), whereas the angle of orientation of the atlas plate shown in C is indicated in situation 2. (C) Line drawing of a reference atlas plate matching the location and tilted to fit the angle of orientation of the section shown in A. The slight difference in angle of orientation between the images in A and B is most easily observed in the hippocampal region, marked with an asterisk. (B) Line drawing of a coronal reference atlas plate, found to be close to the section shown in A. Through the registration process in QuickNII, correctly angled and positioned atlas plates from a 3D rat brain reference atlas (Waxholm Space rat brain atlas) will be superimposed onto each section in the series. The section is one in a series of sections through the brain. (A) Line drawing of an experimental rat brain section cut at an angle slightly tilted compared to the standard coronal plane. S1 Fig: Illustration of DV and ML angle adjustments.
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