TITLE: Creating Custom Brain Slicing Matrices with 3D Printers
AUTHORS: Yosuke Yamazaki, Maki Yuguchi, Keitaro Isokawa

[DESCRIPTION]
To create reproducible brain sections, brain slicing matrices are often utilized. These matrices are designed with anatomically proportioned cavity dimensions and precisely spaced slice channels, enabling consistent and accurate slicing of the brain into coronal or sagittal sections. Brain matrices can be customized for various animal species or developmental stages, and a wide range of models are commercially available. However, there are certain limitations to the variety of these prefabricated products. In this protocol, we design a brain matrix specifically for rodents, tailored to the measurements of the brain sample, and produce the customized brain slicing matrix with a 3D printer.

[STEPS]
SECTION: Mesuratent of the sample
1. The mouse brain sample is placed on the dissection mat.
SECTION: Mesuratent of the sample
2. Following the specified metrics, the approximate length is measured.

 

SECTION: Installation of OpenSCAD
3. For Windows, download the installer from https://openscad.org/ and execute the .exe file to proceed with the installation, or use the following command in the terminal:
 

SECTION: Excute the code for generation
5. Run the OpenSCAD program.

SECTION: Excute the code for generation
6. Choose New button for a new file creation.


 

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7. Copy and paste the code below to the Editor pane on the left side of OpenSCAD window.
 

Review the 3D preview and, if necessary, return to the previous steps to adjust the parameters.
SECTION: Excute the code for generation
9. Push the Preview button on the top of the Editor pane. The outline of the matrix is updated based on the specified values. Review the 3D preview and, if necessary, return to the previous steps to adjust the parameters.

 

SECTION: Obtain the STL file
11. Push the Export to STL icon on the top of the Editor pane. 

 
A dialog box will appear asking for the save location of the STL file. Select the desired save location and click OK.
SECTION: Digital Fabrication
12. Load the STL file into slicer software compatible with the 3D printer. In the following steps, protocols will be provided for using the PreForm to fabricate the design with Formlabs' Form2 printer.
SECTION: Post-processing after fabrication
17. Remove the object from the build plate and either peel off the support material by hand or cut it off with diagonal cutting pliers. 
 

 

SECTION: Digital Fabrication
13. Run PreForm.
SECTION: Digital Fabrication
14. In the menu bar, click File > Open. The Open File window appears. Select the STL file and click OK.
SECTION: Digital Fabrication
15. Configure the orientation of the 3D model and the settings for support structures.
SECTION: Digital Fabrication
16. Select the printer model, material, and layer thickness. 
 

SECTION: Post-processing after fabrication
18. Wash the object with isopropyl alcohol (IPA) for slightly longer than the recommended time for the resin used, in order to remove uncured resin from narrow slots. For more effective cleaning, the use of a magnetic stirrer or an ultrasonic cleaner is recommended.
SECTION: Excute the code for generation
10. Pressing the Render button displays the designed brain matrix on the screen. It may take several seconds for the rendering results to be displayed.

 

SECTION: Post-processing after fabrication
19. Quickly dry the object after removing it from the cleaning solvents, and then proceed with post-curing. Use an air blower to remove any droplets from the narrow gaps.

 



SECTION: Installation of OpenSCAD
4. For macOS, download the dmg file from https://openscad.org/ and install OpenSCAD program from it, or, on a system with Homebrew enabled, use the following command in the terminal:

 

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8.10. font size: The font size for the embossing text can be set.
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8.9. text to emboss: Enter the text or numerical string. A long text will not fit within the designated space.
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8.8. emboss text: Choose either "no" or "yes". Upon selecting "yes," the designated text will be displayed at the top of the matrix.
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8.7. bridge diameter: Define the diameter of the bridge structure as a stabilizer. If the default value of 0.4mm or a similar value is used, it can be easily cut with a razor blade.
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8.6. stabilizer: Add thin rod-like structures that bridge the slots. These contribute to the fabrication stability of narrow slots.
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8.5. shift: When "coronal" is selected and adjustment of the slice position is desired, the slots will shift anteriorly by the specified value of the shift setting. Enter a value that is less tha the value set for thickness.
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8.4. slot width: This item specifies the width of the slot for inserting a razor blade. Although the actual thickness of the razor is thinner, reducing the width of the slot excessively can make the fabrication process challenging.
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8.3. witdth, length, bulb and depth: Input values that are 10% larger than the measurements obtained in the previous step.
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8.2. thickness: The value indicates the slice thickness. The default value is set at 1 (mm). To specify a slice thickness of 2mm, enter 2.
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8.1. direction: Choose either "sagittal" or "coronal". The former should be selected when creating slices that section the sample sagittally, while the latter is chosen for slices that section the sample coronally.
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8. Change the value of the parameters shown below based on the measurement results. The input field is located in the Customizer pane on the right side of the window. 

 

The parameters are: