As mentioned above, the first prerequisite for spine detection is having already detected neurites. We can use either the Neurite Tracer or Neuron Tracer for this task. The Spine Tracer operation can be added immediately after the Neurite Tracer in the pipeline, or after some filtering operations.

The Spine Tracer can use 3 different methods to detect spines:

• AI-Assisted - This method uses a built in DL model for spine detection. This model automatically identifies spines around the neurites with little to no image pre-processing required and can be used in a majority of cases.
• Use Segments - In this case another pipeline operations has already previously segmented the spines and the Spine Tracer is only responsible for assigning the spines to their respective neurites. The spines can be segmented in any suitable method.
• Use Probability Map - Much like for the Use Segments option, we can use any suitable pipeline operation to isolate and enhance the spines from the rest of the image data, but now the segmentation itself is carried out by the Spine Tracer.

These options make it easy for the majority of users to carry out spine quantification with little additional effort while providing the flexibility to address more challenging images.

In every case below the first step is to select the input tag for the trace objects. Most pipelines of this type will only have one tag for the traces, but it is possible to have several tracing operations in the same pipeline, we therefore need to take care to select the correct tag for the traces at this stage.