Cells in Countdown Zone 1 & 2

We have recently completed tracing the 83 cells of countdown phase 1 & 2. Together with 23 cells that had already been completed before the beginning of the countdown, a total of 106 cells in the countdown zone 1 & 2 are displayed here. You can see that the square with 100um-long side is compactly filled up with the somata of the 106 cells.

Of the 106 cells, 58 are ganglion cells and 47 are amacrine cells, while one, the infamous EFC #177, is difficult to figure out. It is roughly estimated that the fraction of amacrine cells in the ganglion cell layer — displaced amacrine cells — is 45%, so our cells match pretty well with it.

There are several well-known types of, as well as uncertain ganglion cells (GCs).

The W3 cells, one of the smallest ganglion cells, account for 6 cells of the 58. As is known, they overlap each other quite a lot. Their primary dendrites arborize near the middle of the inner plexiform layer, and secondary small fraction of the dendrites arborize near the inner nuclear layer.

Another 6 cells are the On-Off Direction Selective Ganglion Cells (ooDSGCs). They come in four subtypes, each of which is responsible for the four cardinal directions of mouse eye (up down forward backward). Still it is not clear which of our six cells belong to which subtype. It is not yet known if there is any way to distinguish them by their anatomical clues or by their connectivity to other cells. This is one of our current research topics.

ooDSGC is a bistratifying cell. There are other kind of bistratifying cells too, it is not yet known how many. Here are shown five different bistratifying cells including the ooDSGC. All of them occupy different levels and the distance between the two levels in each cell varies type to type. 2~6 examples were found for each bistratifying type.

Other cells include one or two of J cells and other cells we are not sure yet. Things will become clearer as we finish phase 3 and have more examples.

 

The amacrine cells (ACs) are usually divided into three (or sometimes four) sub-categories according to their sizes: narrow-field, medium-field, and wide-field cells. see this page for the criteria.

The starburst amacrine cells (SACs) belong to medium-field, may be one of the biggest types of the medium-field cells. 11 On SACs were found in total, only 2 of which were newly traced during the countdown. At the end of the starburst challenge, we estimated that we had identified and traced roughly half of the SACs in the data. It seems like we may have finished more than half by then.

Among other interesting medium-field ACs are 2 very asymmetric cells. The dendrites point only one direction like the J cells do, but no axon could be found for these cells (meaning not a GC) and the direction that these cells point is exactly opposite from the J cell’s. Also, they stratify more narrowly compared to the J cells.

No narrow-field ACs were found from the countdown zone 1 & 2. Narrow-field ACs seem to exist only in the inner nuclear layer.

Wide-field ACs commonly have very long branches but have diverse curvature and complexity. Often we see cells with a few (typically less than 10) extremely straight branches that reach the end of dataset without further arborization. For a cell, on the other hand, because of abundant number of branches and extreme entanglement of them near its cell body, we had to divide it into three parts to trace it conveniently.

A part of the 106 cells were reviewed in this post with less scientific rigor. At the end of the countdown when we finish our mission, our findings will be fully covered and quantitatively analyzed. Until then, let’s keep beating the cells!