What is a good file type for campatibility with blender I have written a program for segmenting fluorescent microscopy images in java. The result are triangulated meshes. I would like to export the meshes to a filetype that is compatible with blender. 

My main criteria is an open API or file structure that I can use.

How can I save mesh data for multiple meshes into a file that blender can read?
I think Wavefront .obj is what you're looking for: https://en.wikipedia.org/wiki/Wavefront_.obj_file

As far as I know, Blender imports an obj file as one single object, so you may have to separate them later.