Usually EyeWire play goes smoothly, but sometimes players come up against tricky cells that may be cause confusion.
Mergers are the most common problem in EyeWire. These are segments that the AI has fused two segments together that don't belong. There is no way for the player to separate these segments, so they must learn to work around them. For small mergers that do not exit the cube a player may ignore them and continue their trace as normal. For larger mergers and/or mergers the exit the cube, the player may leave out the segment with the merger and continue their trace as normal.
Mergers That Exit The Cube
In special cases, the segment with the merger may also exit the cube. In these cases the player should add some "dust" that exits the cube in the same spot as the branch with the merger so that the branch will continue to grow.
Sometimes the merger occurs in the seed. When this happens players should not trace the part of the seed thats a merger. If it is hard to tell which part of the seed is good, players should ask a Scout, Scythe, or Admin for help. If the AI merger exits the cube, a Scout, Scythe, or Admin should be notified as soon as possible.
Sometimes the 2D image slides may contain misalignments. This may cause a "jump" between the misaligned segments. In these cases the player should do their best to look for shape and direction consistency to grow out his or her branch. Identifying reference points in slides and noting how they move can help the player to find the correct continuation of the branch.
Sometimes a misalignment may consist of just a poorly imaged slide, where there will be no discernible branches.
It is important that players utilize multiple visual cues to check their work before they submit. Sometimes pieces look like they fit in the 2D, but clearly do not work in the 3D model. If unclear borders in the 2D plane are causing a player confusion, he or she may also use the command ALT+drag to drag the 2D to a different view.
Tracing through black spills
For various reasons some neurons have been damaged allowing the stain to enter the neurons causing a black spill-like effect in the 2D. It is not always possible to trace through them as sometimes the damage is so extensive that it requires the most expert and experienced of scythes and/or admins to trace through them but some other times it is easier and doable by players.
To trace through such black spills one must scroll through the 2D a number of times adding and removing segments leaving a gap if needed until the neuron is extended to the cube's wall (if that is possible). Sometimes like tracing through mergers leaving a gap is required because adding a segment in the black spill might also add a portion of another neuron which is not desired. It may not look pretty in the end but it may be correct.
File:Blackspill.PNG|400px|thumb|center|A difficult trace through a black spill. Here as can be seen the damage to the neuron/dendrite is extensive for a portion of it.