When we think of Japanese animation, we normally think of two distinct branches, the gorgeously sumptuous delights of Studio Ghibli, or the more visceral thrills of anime. Both could be technically considered one and the same, but to the broader international audience, I think they would be considered separate.
Both demand appreciation from film fans and both have their following, in Japan and internationally. Barring the obvious differences between styles and general content, you could argue the main point of separation between the two is authorship. While Studio Ghibli is synonymous with Hayao Miyazaki and is often considered one and the same, anime is a much more open and far-ranging proposition.
There are numerous studios, including Madhouse (famous for Ninja Scroll and Trigan), Tms Entertainment (Akira) and Production I.G.