In your current pipeline, I saw that you used module ApplyThreshold combined with Automatic thresholding in IdentifyPrimaryObjects. This is not a recommended practice. Instead, you could use IdentifyPrimaryObjects with thresholding method Adaptive Otsu, especially when you have bright / dim shades of neurites like this.
Also, as mentioned in this topic , it’s better to first recognize the bodies of the neurons as the primary objects, then use them to find neurites as secondary objects.
Your first attached image was not the original image, it’s a .png saved by CellProfiler. I’ve tried to work on it nevertheless to build this pipeline, can you try to fine tune it with your original .tif image measure_neuron.cpproj (641.2 KB), pay attention to the size of your objects and the size of filters in EnhanceOrSuppressFeatures