Fig. 2.

Schematic overview of the processing steps in NeuronMetrics. Square brackets indicate optional steps and asterisks indicate steps that require user input. Main modules (bold text along left side) are run by selecting them under the ImageJ “Plugins” [sic] menu. When processing a batch of images with the Neuron & Cell Body module, Neuron ROI, Noise ROIs, and Click Cell Body run sequentially on each image in the folder because the user performs a brief manual task in each step. Subsequently, all images in the folder are automatically run through Cell Body ROI. Thereafter, the user initiates the desired module, in sequence, to process all images in the folder in batch mode.