Common User Errors in the Minnie Dataset

In this tutorial we’ll go over some common user-created proofreading errors in Minnie. Learning to identify these types of errors can greatly improve your proofreading accuracy!

Branch morphology

As you’re searching for branch continuations while proofreading, make sure you are taking a holistic view of your cell. While you of course want your EM slides to match up, you also want to make sure your 3D meshes look correct.

While proofreading in Minnie make sure that:

• Branch continuations have similar thicknesses, direction, and structural features to the segment they are joining with
• Branches should taper from thick at the base, to thinner at the branch end. If your continuation shows inconsistent thickness, this may be a clue that it is incorrect.

Take a look at the continuation on this branch. Let’s identify clues that may make us want to give it a second look.

Does it have…

Although some features of this continuation make it seem like it could belong, upon further inspection we see that it does not meet all the criteria for a proper extension.

Use synapse clues when making connections

If you are unsure about connecting segments in your cell, you can check their synapse points for congruency.

Synapses are the junctions between two neurons where communication occurs. When activated, one neuron sends neurotransmitters to the partner cell at these junctions. The synapse is made up of the pre-synaptic partner, which contains vesicles that hold the neurotransmitters, and the post-synaptic partner which receives the signal.

The cells we are tracing – excitatory pyramidal cells, send signals via the axon, which are received by dendrites on other cells. These cells make up 80% of our dataset.

The cells we are not tracing are called inhibitory cells. They come in a variety of cell types, but overall make up a much smaller proportion of the dataset.

Excitatory synapses have different internal structures and post synaptic densities from inhibitory synapses. You can check the synapse types on a branch you are working on to help determine if you have a merger or not. Here are some questions you might ask:

• Does my side of the synapse contain vesicles? If you are extending an axon branch, you should see vesicles on your side at the synapse points.
• Is this an asymmetric synapse? If you are extending an axon on an excitatory pyramidal cell, you should be finding asymmetric synapses at these junctions. (More about this below)

If you answered “no” to either of these questions when proofreading an axon on a pyramidal cell, you should look for a merger along your branch.

We’ll now go over excitatory vs inhibitory synapses to help you identify each type when proofreading.

S – Asymmetric Synapse (Excitatory cells)

• Has a thick post-synaptic density (PSD)
• Vesicles (objects inside cell) are large and round

F – Symmetric Synapse (Inhibitory cells)

• Has thinner post-synaptic density (PSD)
• Vesicles (objects inside cell) are generally smaller, and may be multiple shapes (round, flattened, oblong)

Images from The University of Texas at Austin. Image 1. Image 2.

Can you guess which type of synapse the following examples are?

You can take a closer look at these synapses here. Cells are colored differently from above images to differentiate between cell types.

Problem solving difficulties when proofreading

Here are some examples of difficult errors that were solved. These results videos may help you to identify similar issues you may encounter when proofreading.

Minnie Proofreading Demo