To trace the morphology of a neuron from a confocal z-stack, open the stack in Fiji. Launch the Simple Neurite Tracer plugin (Plugins -> Segmentation -> Simple Neurite Tracer). Instructions for using the Plugin are posted here. When tracing, it’s helpful to selecting the viewing option “View Paths (2D): parts in nearby slices”. Draw paths through all the neurites of the neuron. The paths do not need to join up if you goal is simply to create a visual representation of the fill (and not to do any quantitative analysis on the fill) – the tracing does not need to represent a single unbroken skeleton, and so it’s adequate for the endpoints of two paths to be extremely close. Save the skeletonized path file (File -> Save traces file). Then use the Fill Out command to automatically generate a 3D volume around the skeleton. Select all the paths from the list (in the All Paths window), and select the “Fill Out” button. Fiji will search for the boundaries of the fill, and you can set the threshold for the boundary as a free parameter (with the Set button). The algorithm does not need to converge – you can pause the process if it stalls and still potentially recover a satisfactory fill. It’s useful to try a few boundary settings to determine what result best resembles the original fill. Save the fill for further processing. The fill will render as a white neuron on a black background; you can then open the z-projection in Photoshop and invert the colors in the image to obtain a black neuron on a white background.