CellProfiler comes with a toolbox specifically for C. elegans assays, so this may fit the bill. Go to cellprofiler.org/examples.shtml, and look under “Pipelines using the WormToolbox” to see example images and pipelines. We also have a Nature Methods paper describing the workings of the algorithms involved: go.nature.com/D4H5E2.
Now, not having seen your assay, it may be that what is described here is excessive for your needs. But it shows that once a worm is identified (by whatever means), intensities from another channel can be use to produce measurements along with worm axis. Alternately, if you are simply interested in overall reporter intensity, the MeasureObjectIntensity module can be used once the worm is identified.