Microcosm experiments usually requires laborous counting and measuring procedures. For many laborotory model organisms such as the Collembola and soil mites, sampling population and trait dynamics requires extra efforts as their movements are prone to small disturbances. Using image-processing tool and automatic repeating procedure, I developed an automatic counting procedure with ImageJ plugin.

A contracting background can be removed using at least three photos, and further steps involve area alignment, particle filtering, etc, accroding to standard ImageJ processes. Using mutiple loops coded in Java, this process can automatically process thousands of pictures and return csv data at the same time!

A pre-coded ImageJ plugin for measuring number and size can be Download and modified by users.

In one of the previously finished microcosm experiments, I monitored patch-specific, weekly population and size and variation for nine months. This is a four-patch system with or without good corridor connectivity, simulated environmental stress, and species recovery after exposure. If anyone is interested in these data for parameter models, please contact to me for details.