I will try to explain the use of the plugin. So if MiToBo is running and you select the NeuronAnalyzer2D a configuration window is opened for the NeuronAnalyzer2D operator.
First you con configure the detector for neurites. Allow for profile extraction, define molecule names of the different staining channels in the image, select the index of the molecule channels for profile detection along neurites and if present you can try to detect particles along the neurites, which may not work probably on all images.
Think the important step is the Neurite Detector configuration. If you select the button a new window comes up. On top, go to view -> advanced to see all parameters.
Choose the directory with your input files, define nuclei channels. Of course there are a lot of parameters, which are predefined for the images we used. On the MiToBo website you can find some example images, maybe it is a good starting point to try the operator with these images. Did you get the operator running and there are some errors?