Eyewire II

Quick Access

All Cells except BCs All BCs Researcher Spreadsheet Cell Type List preliminary Morphotyper Functional data

Functional data includes calcium responses of ca. 400 GCL cells. If you cannot see that repository yet, send your GitHub username to support@eyewire.ai.

Main Cell Spreadsheet

The All Cells spreadsheet holds tracked cells except BCs, most of them proofread. The All BCs spreadsheet holds tracked BCs, including some proofread cells, and predicted locations of their ribbon synapses.

You can open the All Cells and All BCs spreadsheets from Quick Access. They are currently read-only; use the tabs at the lower left of the spreadsheet to switch between the two sheets when viewing the shared workbook.

A cell generally counts as proofread when the ends of all neurites have been manually inspected and confirmed as true ends. A proofread cell is typically annotated like this example cell.

Nuc Coords: x,y,z coordinates of the cell nucleus.
Soma Coords: x,y,z coordinates of the cell soma.
Status: Whether proofreading is work in progress, completed, or problematic.
Proofread Link: Link to the state directly after proofreading, which may not be the latest state.
Proofread Nuc ID / Proofread Seg ID: The nucleus and cell segment IDs after proofreading.
Latest Nuc ID / Latest Seg ID: The most recent nucleus and cell IDs; Latest Seg ID should be used for analysis.
Cell Class/Type: Human annotation, when available. Community annotations can be added through the researcher spreadsheet.
Cell Class/Type machine: Random forest classifier prediction. It is regularly updated and should be used with caution for rare or unusual types.
Confidence Cell Class/Type machine: Confidence measure for the classifier prediction.

Researcher Spreadsheet

The Researcher spreadsheet is where community members can contribute cells and annotations. It contains cells added by the community, including fully proofread cells and work in progress. You can add cells that you have proofread and/or typed yourself, and the team regularly syncs the researcher spreadsheet with the main spreadsheet to make those contributions available to the community.

While the automatic segmentation often looks good already, every cell should eventually be manually proofread to ensure that it has been correctly segmented. Before adding a cell, please make sure it does not already exist in the main or Researcher spreadsheet.

When adding cells, follow the correct format for each column and complete all relevant fields, at minimum Coordinates, Proofreading IDs, Proofreading Link, Proofreader, and Status. The Researcher Instructions tab of the spreadsheet contains detailed proofreading instructions. For cells where proofreading is not complete, add Initial IDs and coordinates, then set Status to Need help.

Not all columns need to be filled out for each cell, but please include the following when they apply:

Nuc Coords: x,y,z coordinates of the cell nucleus, if there is one.
Soma Coords: x,y,z coordinates of the cell soma or trunk.
Status: Whether proofreading is work in progress, completed, or problematic.
Proofread Link: If proofread, include the link with endpoint annotations.
Proofread Nuc ID / Proofread Seg ID: The nucleus and cell segment IDs after proofreading.
Proofreader / Cell Typer Name: Add your name here.
Cell Class/Type: Add the cell class and type you identified.

To get edit access, open the spreadsheet with your Google account, click the View access only button on the top left, then click Request access in the pop-up. Access is typically granted within the next work day.