Sprite Packer running out of memory

Hi. I am converting an old project to Unity which has a lot of sprites. There are over 4000 sprites and I have organized them into 81 atlases. Does Unity need to load every single one of these into memory at the same time in order to pack them?

When I attempt to pack the sprites I get to around the 2000th sprite and then crash due to running out of memory (task manager reports 3.5Gb). I'm really confused about what is going on. The only information I can find about this is an issue in Unity 4.3 that was already fixed. I am using 4.5.2. on Windows 7 64-bit.

Can someone help my find a better way to pack my sprites or figure out what's going wrong that causes unity to take so much memory?