We have a similar issue with the transverse slices we get for the study of the hippocampus, in the sense that we need the slices to be cut at a specific angle to preserve CA3-mossy fiber function.

Now, what you can do depends on the slicing protocol you follow. In our case, once we have extracted the brain and before we stick it to the slicing chamber, we use a blade to cut the top of the brain in the exact angle we need and provide a flat surface that will make the brain stable during the slicing at that angle you need. Of course in our case it is easy because the angle is relatively small, but in you case being 45° that would mean getting rid of a lot of useful tissue.

I hope that helps.

Thank you Daniel 

That was very useful ... I am still looking for the best protocol to use, because we have never done anything similar in my lab and I thought that trying this method can open up a ideas for new projects. Since you have already established this method, can you tell me about the protocol you are using?

Instead of cutting your brain, another way to do this is to cut an agarose block at a 45 degree angle and resting your brain on that. This is fairly easy to do with the Compresstome, but should be able to be done on other Vibratomes as well. This way, you are not cutting out any brain.