Tracing and measuring neurites using NeuronJ

SLIM interfaces easily with NeuronJ

NeuronJ is an ImageJ plugin developed by Meijering et al. [2]. The plugin can be found in the 2D analysis menu, and once run, a new toolset on the main ImageJ window loads. NeuronJ allows the user to easily trace along neurites and performs measurements for parameters such as the length, mean value along the trace, and many more. Moreover, the traces can be saved as a text le consists of the coordinate and values of the points along the trace, and allows the user to treat the data as a list of values instead of a complex structure.
1. Convert the SLIM map to an 8-bit image and save
2. Run NeuronJ found in 2D analysis menu and load the 8-bit image using NeuronJ “Load images”
3. Trace neurites using “Add tracings” in NeuronJ
4. Run measurements using “Measure tracings” in NeuronJ