Countdown 2: The Dig

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At long last…

The wait is over.

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In October 2014, Eyewire began a countdown of cells in one area of our data set: The Countdown to Neuropia. This was finished in July 2015, and since then, a lot of you have been wondering, “What’s next for Eyewire?”

Wonder no longer, for our neuroscience team at Princeton University has delivered us a whole new selection of cells to discover. You tested some of these cells for us when we put up the Lab Cells a few months ago; now we have the data and the tools prepared to tackle every last cell of the batch. It’s an interesting little challenge, though, because we don’t know exactly how many types of cells are in this sample of the retina or how they’re connected. They are packed together very densely indeed, too densely to count all cell bodies in advance.

To that end, HQ has decided to treat this sequence of cells less as a “countdown” and more as a “count-up.” We’re dividing the region into a grid, creating 16 sectors to map from the inside out, and just like an archaeological site, we’re going to work sector by sector until we’ve found and traced every possible neuron. Hence our name for this process: The Dig.

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Each sector measures 50 x 50 µm (microns). In each sector we then know there are more or less a couple hundred cells, but again, we won’t be certain till they’re reconstructed. Generally, though, this means we have well over 2000 cells to map before the Dig is complete. If you think that sounds like a lot, it is! At our current completion rate, it would take us at least two months to finish a sector, and thus more than two years to finish everything. However, we aren’t just excited about the Dig because it’s something new. As the Dig progresses, we intend to be regularly rolling out awesome improvements to Eyewire’s infrastructure, mechanics, and overall user experience; all of these changes should make the game more fun, but they’re also going to make us finish cells at a substantially faster rate.

Thus… just like we don’t have a precise count of cells, we don’t have a precise end date for this project, but you can rest assured that it will not be 2018 by the time we’re done! It will be great to see how quick we become.

Additionally, each cell will have its screenshot placed in a designated album for each sector on our Facebook page, so that if you like, you can look at all the cells in a sector at once.

What to Expect From Dig Cells

  • More starburst amacrine cells! A perennial Eyewire favorite.
  • Bipolar cells. After testing with the Lab Cells, we are now confident that you’re ready to tackle their unusual cauliflower-shaped formations.
  • Overall, as was seen with the Lab Cells, many of these cells are tiny, nubby, bouton-covered, and flat out weird. They’re like nothing we’ve seen before!
  • In the spirit of archaeology, cells will be called Artifacts for Level 1 (formerly Mysteries) and Relics for Level 2 (formerly Lightnings).
  • Cells will be numbered by sector number and cell number together. For instance, the first cell in Sector 2 could be Relic 2.1, the twenty-third cell in Sector 9 could be Artifact 9.23, etc.

More on the Science

Side views of EyeWire data. Top: Countdown Zones in the GCL vs The Dig Sectors in the INL. Middle: a type of GCs. Bottom: Displaced Starburst (blue), normal Starburst (red), and a BC (green).
Side view of the EyeWire data. The entire Countdown Zones in the GCL vs the area of 16 sectors of The Dig in the INL.

The mouse retina comprises layers. Among them, EyeWire includes the Ganglion Cell Layer (GCL), Inner Nuclear Layer (INL), and Inner Plexiform Layer (IPL). They form sandwich-like structure as in the image above. The top and bottom “bread slices” are the layers of cell bodies, whose cross section appear as large circles. The center “spread” layer is where the branches from all those cell bodies arborize and are entangled with one another to form synapses.

Side views of EyeWire data. Top: Countdown Zones in the GCL vs The Dig Sectors in the INL. Middle: a type of GCs. Bottom: Displaced Starburst (blue), normal Starburst (red), and a BC (green).
Side view of seven GCs of a single type.

The two cell body layers comprise different sets of neuron classes. Countdown to Neuropia targets the cells of the GCL. This layer contains cell bodies of the Ganglion Cells (GCs), the axons of which converge to form the optic nerve and send visual information from the eye into the brain. The GCL also contains “displaced” Amacrine Cells (ACs).

A displaced Starburst (cyan), a normal Starburst (yellow), a BC (pink), and a GC (green).
A displaced Starburst (cyan), a normal Starburst (yellow), a BC (pink), and a GC (green) forming a direction selective circuit.

With The Dig, we are conquering the INL, the cell body layer of “normal” ACs and Bipolar Cells (BCs). The BCs are the only input source from the outside to the IPL. They provide excitatory inputs to the ACs and GCs. The ACs interconnect all the cell classes above and make the neural circuits more complex. By playing the INL cells during The Dig, we will finish the second half of the cells to map their circuits in the IPL.

Super Science

The cell bodies of the INL are smaller than those of the GCL. In addition, the INL is 5~6 cell bodies thick while the GCL is only 1~2 cell bodies thick. As a result, a given area of The Dig contains 4~5 times as many cells as the same area in the Countdown to Neuropia. For example, while the Countdown Zone 1 at the center of GCL contains 27 cells, the same area at the center of INL contains 118.

To show just how many cell bodies are even in the GCL, here is the video using our completed data from the Countdown to Neuropia:

The ACs have much higher variability than the GCs. They can be smaller than the smallest GCs and larger than the largest GCs. A similar thing could be said about the complexity of cell structure or the difficulty of playing. Scientists only speculate that there can be 2~3 times as many types of ACs as the types of GCs, but they do not know the exact number yet. We should be able to nail down the number after the Dig. So please enjoy the game and teach the scientists a lesson.

Marathon Launch

We break ground on Wednesday 1/27 at 10:00 AM EST, beginning with our January marathon cell. You’ll see a post with marathon details in a few days. Grab your shovels, brushes, and pickaxes… because the future of neuroscience is now!

EyeWire, The Dig, citizen science, neuropia

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