The FlyWire connectome contains over 127,000 proofread cells, ~73,000 of which are in the optic lobes (OL). While ~50,000 cells in the brain have labels, as of this post (May 2023), only 27% of neurons in the optic lobes are labeled (~20K cells). We hereby request the help of all FlyWire community members to complete the connectome by adding the missing optic lobe tags.
Using existing labels, we tried to predict candidates for the numerous unicolumnars (cells that appear once in each eye/ommatidia). Find cell type predictions on the new Codex Optic Lobe Tagging Dashboard. The column titled Candidates contains possible unlabeled neurons for each type in both left and right hemispheres. Click the candidates to open list view. You can then view cells individually or download IDs to work through them in chunks. Lists are updated every 24 hours.
L1-L5, Mi1, Mi4, Mi9, Tm1, Tm2, Tm9, Tm20, Dm2, Dm8, T1, T4a, T4b, T4c, T4d, T5a, T5b, T5c, T5d, C2, C3, R7, R8: ~ 790 on the left side and 780 on the right side.– Emil Kind
For a complete list, descriptions, images, and links, see the full Flyer Optic Lobe Cell Guide. This link also contains helpful neuropil layer references for cells such as T4 and T5.
Check out the Labeling Leaderboard page in Codex for the latest on the whole brain as well as top labelers and labs. Congratulations to the Flyers repping lab Eyewire for holding down first place among all labs and to KrzysztofKruk, annkri, and AzureJay who entered into the Optic Lobe Tag rally among the top 15 labelers of all time in FlyWire.
Addons to expedite neuron labeling
FlyWire’s volunteer dev and citizen scientist participant Krzysztof Kruk has kindly created a number of addons that aid in the proofreading and labeling of FlyWire cells.
Here are a couple that you may find useful for the Tag Rally.
Cell Identification Helper
The Cell Identification Helper plugin speeds up the process when labeling individual cells or groups of cells. It also allows for uniform syntax, which is useful when scrubbing through cell labeling data.
For labeling individual cells you can simply click on the lightbulb for any cell ID, and then click the purple “Identify” button. Once the plugin is enabled, this will bring up a list of labels for you to choose from. Simple choose the desired item from the list, and then type in any suffix desired into the “suffix” box. It will format your cell label for you automatically.
You can also batch label cells using this plugin. To use this feature, enable the addons dock and click the “Get cells” button.
Type your desired label into the text box and click “Save.”
Now position your axes into a cell you wish to label. Press the (/) or (-) key on your keyboard. A green box will appear in upper right hand corner of your screen to indicate that your label has been successfully submitted.
Repeat this process for all desired cells.
Once you’re finished, click the “Get cells” button again. You will have the option to submit labels for individual cells or for all the selected cells at once.
This plugin has many features, but let’s highlight a few that you may find useful for this task.
You can begin using the batch processor by opening the “actions” menu at the top of the screen.
“Change color for (visible/all)” will allow you to recolor certain cells with any desired color. This feature can be very helpful for tracking certain cells, or sharing links with others.
“Find common partners for visible” will enable you to find synaptic partners with one or more cells that you are investigating. This can help you identify related cells and speed up the tagging process. For example, if you have a known L1 cell, finding its synaptic partners can help you uncover related L2-5 cells, some of which may not be tagged yet.
“Show statuses and labels for (visible/all)” can also help with the labeling process. This gives you aggregated information on the labeled statuses of cells you are currently working with. From here you can pick out cells that have already been labeled by others which may aid you on your tagging adventure.
These addons will be the most beneficial to you during the Tag Rally, but there are additional addons created by KK that you may also wish to download!
See this post for a comprehensive list of addons and more detailed instructions on using the addons listed in this page.
Thanks for being a part of the FlyWire community!
Thanks to Emil Kind for advising on optic lobe neurobiology.