The current version of the notebook looks like this:

The design has in my opinion too many bounding boxes and appears still overloaded. The tool buttons attract too much attention and appear misplaced when overlapping the editor field. Therefore I suggest the following more clean and simplistic design:

In summary:

• Line numbers are outside the cell and appear only at the selected cell.
• Controll icons are on the right and also appear only at the selected cell.
• The background for the Python code is dark as in standard Jupyter-Notebooks and white for the output (at aleast for the bright color theme). This is more optimal for plots that normally have white background.
• The execution counter (like [2]) is inside and grouped together with the timing information so that it is not confused with a line number.