Using a custom annotation atlas in Neuroglancer
The Brody Lab at the Princeton Neuroscience Institute is in the process of developing a detailed rat brain atlas for interpreting their data from whole brain microscopy, analogous to the Allen Mouse Brain Atlas. The goal is to start with an existing MRI-based atlas that has only basic, large brain structures and add finer structures. This process is iterative and requires redrawing brain region boundaries and then visualizing the re-drawn atlas at each iteration. The Brody Lab was interested in using Neuroglancer for visualization of this process.
Up to this point, we had been using Neuroglancer in BRAIN CoGS to view atlases whose region labels are static, such as the Allen Mouse Brain Atlas and the Princeton Mouse Brain Atlas (Pisano et al. 2020, submitted). However, visualizing an atlas in Neuroglancer where you provide custom labels for the regions is also possible. In this jupyter notebook, we go through how to do this using the rat MRI atlas as an example. One could use the procedure in the notebook for any custom text labeling of segments in Neuroglancer.
If you are brand new to Neuroglancer, I recommend you start with our getting started with neuroglancer post and associated jupyter notebook before diving into this example.