This protocol presents the methodology for creating affordable and easy-to-build brain matrices that can be used to aid in the slicing of the piglet brain or any other species of large animals at the desired orientation and thickness. Importantly, as opposed to commercial "fixed-size" matrices that work with only a limited range of brain sizes, this approach allows the matrix to be conveniently adjusted or expanded to fit a wide range of brain sizes. In this report, a matrix built for a 30 g piglet brain was successfully expanded to accommodate a brain 80% larger, with a snug fit to facilitate accurate brain slicing. It is recommended that the addition or removal of acrylic plates be done symmetrically to maintain the brain midline orientation for the sagittal cutting matrix, but not necessarily for the coronal matrix, because of the relatively uneven growth ratio among brain regions. Moreover, this matrix fabrication method can be applied to other large animal species such as monkeys, sheep, canines, cats, and ferrets.
In the current method, brain casts are used to create templates. An alternative is to use MRI images to create the serial template. Several longitudinal MRI scans to investigate piglets' brain development have been obtained previously2 or as part of this study. Although MRI is a very precise and flexible method to study brain anatomy and development2, the established database of pig brain MRI imaging covers between 2 and 24 weeks of age2, lacking the data of the first 2 weeks of brain growth, which is critical for neonatology studies. Moreover, it is not easy to create precise templates based on MRI imaging at a millimeter scale, and the 3D brain scanning requires a specialized device and software14. In comparison, based on our templates that were created on millimeter-scale paper, those acrylic plates can be precisely cut, carved, and polished by hand, or using a computerized automatic acrylic cutting or engraving device. Alternatively, 3D printing technique can be utilized to create individual plates or the whole matrix as one piece14,15,16, after the computerization of templates.
Since the stacked acrylic plates were cut from a large piece, the dimensions of each plate may vary a little. Thus, we aligned them to the left lower corner, which is considered as "0,0" in the axis and the reference point for the anchoring holes and the copying of each template. It is critical to keep the orientation consistent when copying each agarose slice to the scale paper to establish the template, as well as copying the templates to the acrylic plates. Labeling "anterior" and "posterior" clearly on each of the templates on the scale paper, numbering successive slices, and marking a color line on one side of the acrylic plate after the three anchoring holes were drilled, assists in constructing an accurate matrix.
Trimming and polishing of the carving lines are necessary on all the acrylic plates. This step can make the cavity of the matrix fit the brain more closely, providing better support when slicing, and smooths the edges to avoid rough edges that could damage the brain. It may take several rounds of "fit and fix" to make sure the cavity adapts to the brain properly, without many bulges or humps at the bottom. In addition, the uneven bottom of the matrix that was created from the brain cast fits the brain's bottom better, providing better support during the brain slicing. Based on our observation, in contrast to the complicated and significant cortical gyri and sulci development along the first few months, the geometry of the brain bottom does not change dramatically, except for size expansion. Therefore, the matrix can be more easily transformed to fit various brain sizes by adding proper plates, although the brain positioning or plate shape may need adjustment. Moreover, the current design keeps the brains upright when they are fitted into the matrix to minimize deformation or injury to the cortex, which is our study focus. The researchers can customize their brain orientations during agarose embedding and template building to create matrices that can accommodate different research needs -- placing the cortex towards the bottom of the matrix cavity.
It is critical to secure the brain properly in the matrix cavity during brain slicing. Our best practice is to use one hand for slicing, with the other hand gently pushing the brain downwards and towards the brain stem end for coronal slicing, or the lateral wall of the cavity for sagittal slicing. With the snug fitting of the bottom and side wall, as well as the guidance of the cutting blade from the thin gaps between each plate (~0.5 mm), the thickness of each slice is very consistent (Figure 6B,D). Importantly, although we built dedicated coronal or sagittal matrices that fit the whole brain, the brain can be divided into two hemispheres and used for coronal and sagittal slicing, respectively, when the brain is naïve or receives diffuse, widespread stresses, like asphyxia. This "one hemisphere" cutting method requires some experience and extra steps in supporting and securing the brain in the matrix, like adding an agarose block that was trimmed to fit the empty space of the matrix, but it provides a very efficient way to generate more research materials as needed. We have successfully dissected out the subventricular zone from 5 mm-thick coronal slices for whole mount staining, and the hippocampus from both coronal and sagittal slices for further analysis.
In conclusion, this protocol has established an easy, cost-friendly, and flexible method to create brain matrices for neonatal piglets. This concept can be applied to create matrices for older pigs or other large animal models.