Notebook Cell References

Goal

Communicate clearly about Jupyter notebook cells without confusing the user.

What Failed

• •Referring to cells by number (e.g., "Cell 9", "Cell 12")
• •Cell numbers are NOT visible in Jupyter notebooks
• •Cell numbers change when cells are added/deleted
• •User has no way to know which cell you mean

What Works

Refer to cells by identifiable characteristics:

1. •Section header: "the cell under '## Load Data'"
2. •First line of code: "the cell starting with sc.read_h5ad(...)"
3. •Purpose: "the normalization cell", "the plotting cell"
4. •Variable defined: "the cell that creates protein_shared"
5. •Function defined: "the cell with def detection_aware_normalize"

Examples

Bad

• •"Update Cell 9"
• •"The error is in Cell 12"
• •"Cells 10-12 need changes"

Good

• •"Update the normalization cell (starts with # Normalize shared features)"
• •"The error is in the visualization cell that plots histograms"
• •"The cells between 'Load Data' and 'Run Integration' need changes"

Trigger

When discussing or modifying Jupyter notebook cells.