How to annotate an event

This guide shows you how to annotate a single-cell event, either for manual characterisation or to create a dataset to train a deep learning event detection model.

Reference keys: event, event class, event time

Prerequisite: You have accurately segmented, tracked and measured a cell population of interest. This guide only applies to dynamic data.

Prepare the viewer

  1. Go to the DETECT EVENTS section for the cell population of interest. Click on the button to set up the viewer.

  2. Set the modality to “grayscale”.

  3. Set the channel of interest.

  4. Adapt the fraction value to your data (e.g. 0.25). At a fraction of 1, you will see the original image (but the viewer will take longer to open and may be slow).

  5. Set a time interval between frames (e.g. 100 ms).

  6. Save and exit.

Annotate in the viewer

  1. Press the button of the DETECT EVENT section to open the event viewer.

  2. Adjust the image contrast.

  3. On the top-left side, create a new event by pressing the button.

  4. Give the event a name and set the initialization class to “no event”.

  5. Click on a single cell to modify its event class.

  6. Press correct on the left side to change the class. Choose a class among “event”, “no event”, “else” and “remove”. If you pick “event”, determine the exact time (in frame unit) at which the event occurs. Use the time-series of the single cell to observe inflexion points and determine precisely this time.

  7. Click on submit, a vertical line will show you the event time on the time series.

  8. Proceed to annotate all single-cells with the proper class.

  9. Press the button at the bottom of the left side to export a time-series dataset (in .npy format). Put the file in a folder containing all of your annotations specific to this event.

  10. Press the Save button to update the position table with the new event class and the values for each cell.

Viewer Controls & Shortcuts

The Event Annotator provides controls to play animation, jump between frames, and quickly annotate cells using keyboard shortcuts.

For a complete list of shortcuts (e.g., Space to play, n for no-event), see the Signal Annotator Shortcuts.

Interactive Correction

For efficiently refining annotations, you can use the Interactive Plotter to visualize and correct multiple events simultaneously based on their signal traces.

  1. Open the Plotter: While the Event Annotator is open, press Ctrl+P or select View > Interactive Plotter from the menu.

  2. Visualize Signals: The viewer displays the signal traces for all loaded tracks, centered on their annotated event time (t=0). You can change the displayed signal using the dropdown menu.

  3. Select Tracks: Click and drag to draw a box around traces of interest. Selected traces will be highlighted in red.

  4. Shift Event Time: Use the Left and Right Arrow keys to shift the event time (t0) for the selected tracks. The curves will move horizontally to reflect the new alignment.

  5. Batch Reclassify: Use the buttons at the top to assign a new class to all selected tracks:

    • Event: Confirmed event (Class 0).

    • No Event: Reject as noise or non-event (Class 1).

    • Left-censored/Else: Ambiguous or other event type (Class 2).

    • Delete: Mark for removal.

  6. Save Changes: Press Save Changes in the plotter to save your corrections to the disk. The main Event Annotator window will update to reflect these changes.