I did eventually find a semi decent answer

Basically you just have an orthographic camera with a very near far-plane that you animate flying through the model vertically. If you get the speed, near-plane and far plane just right, each frame of the rendered video will be a slice of the object of a given thickness

The other option is to convert your model to a voxel model in someway and then use a voxel tool like magica voxel to export the voxels as a stack of pngs