How to plot the 3d brain in Fig5d?

[Smilenone]

Thank you for your incredible work, which has been a great source of inspiration for me. I was wondering how to visualize a 3D brain in Fig 5d and how to display the coronal, sagittal, and transverse views. Could you release the code on this?

[pangkun97]

For the 3D visualization of markers in different brain regions shown in Fig. 5, the data can be filtered based on regional information. Using the k3d library, the k3d.points function can be invoked multiple times to assign unique color parameters to each brain region. This allows all regions to be displayed within the same 3D brain model while maintaining distinct visual identities.

To visualize cross-sections, you can constrain one coordinate axis (e.g., the x-axis) to a narrow range for data filtering. Then, using the other two axes (e.g., y and z axes), you can generate 2D plots to represent different sectional views.

The visualization code for this workflow is available in the MAGIC-seq/Analysis-code/Mouse_Embryo_Brain_3D.ipynb file.