Workshop quick reference

Workshop quick reference#

Keep this page beside you during the workshop.

Start and stop#

Open PowerShell (Windows) or Terminal (macOS), move into the workshop folder, then:

uv sync --locked
uv run jupyter lab

Open notebooks/01_rendering_workshop.ipynb. Select Python (napari workshop) at the upper right. JupyterLab is in the browser; napari is a separate window. To finish, save the notebook, close napari, then choose File → Shut Down in JupyterLab.

Where things are#

Item

Location

Main lesson

notebooks/01_rendering_workshop.ipynb

Setup check

notebooks/00_check_setup.ipynb

Teaching data

data/teaching/

Screenshots and movies

outputs/

Help

setup/troubleshooting.md

Notebook controls#

Goal

Action

Run selected cell

Shift+Enter

Run from a clean state

Kernel → Restart Kernel and Run All Cells…

Stop a stuck cell

Kernel → Interrupt Kernel

Confirm Python

Run import sys; print(sys.executable); path should contain this folder and .venv

Save code and notes

File → Save Notebook

Run cells from top to bottom. [*] means Python is busy; a number such as [7] means the cell finished.

Napari controls#

Goal

Action

Select a layer

Click its name in the layer list

Show/hide a layer

Click its eye icon

Change contrast

Adjust contrast limits for the selected image layer

Change color

Select a colormap

Combine light from layers

Set image blending to additive and adjust opacity

Move through time/depth

Drag the t or z dimension slider

Switch 2D/3D

Click the 2D/3D display button

Pan

Drag with the pan/zoom tool

Zoom

Mouse wheel or trackpad scroll

Reset view

Press Home

Display controls change what you see, not the stored voxel intensities. A maximum-intensity projection keeps the brightest value along depth and discards where that value was along z.

Coordinates and meaning#

  • Images, detections: t, z, y, x

  • Tracks: id, t, z, y, x

  • t is a frame index from 0 to 29, not confirmed seconds.

  • Spatial coordinates are source voxels, not confirmed micrometres.

  • A point is a supplied candidate detection.

  • A track is a supplied association of detections across frames.

  • Track tail length is a time window; it is not the number of particles.

  • The prepared data are reduced fourfold in space, so fine detail is lost.

Recovery#

  • No napari window: look behind the browser or use Alt+Tab/Command+Tab.

  • Wrong result: restart the kernel and run all cells in order.

  • Missing data: confirm data/teaching/metadata.json exists.

  • Slow/blank 3D: use the 2D or projection route and pair for the 3D activity.

  • Movie fails: keep the PNG screenshot and use the reference movie.

  • Download exceeds five class minutes: use the instructor’s local copy or paired route.

  • Existing output folder: choose a new output name; do not mix old and new frames.

Teaching dataset: https://doi.org/10.5281/zenodo.22696913. Original source: https://doi.org/10.5281/zenodo.22694247. Both CC BY 4.0.