TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets.
An ImageJ plugin (author: Kurt De Vos) for counting multiple cell classes manually, which overlays already-counted cells on the image. It is controlled via its own graphical user interface, and can export and load results.
