Add per-channel visibility checkbox (temporary on/off)

[yulewu]

Feature request

In the channel controls, add an on/off checkbox next to each displayed channel to temporarily hide/show that channel without removing it from the current channel selection.

Motivation / problem

UELer’s UI includes a “Channel Selection” workflow (with multi-select behavior, e.g., holding Shift) that determines which channels are shown. Users often need to quickly toggle a single channel off (e.g., to check bleed-through, verify colocalization, or compare overlays) and then toggle it back on, without losing the current multi-channel selection state.

Proposed behavior (UX)

• In the channel list/panel, render a checkbox per channel row:
  • Checked = channel is visible in the viewer (and any linked visualizations that use the current displayed channels).
  • Unchecked = channel is temporarily hidden, but remains selected (so it can be re-enabled with one click).
• Toggling should be fast and not require re-selecting channels.
• The toggle state can be session-scoped by default (no persistence required unless easy to support).

Acceptance criteria

• Each displayed channel has an on/off checkbox next to it in the channel controls.
• Unchecking a channel removes it from the rendered composite/overlay immediately (or on next redraw) without altering the underlying “selected channels” set.
• Re-checking restores the channel with its previous color/range settings.
• Behavior works when many channels are selected (typical MIBI panel sizes).
• No regression to marker set loading / channel palette behavior.

Validation steps

1. Launch the viewer via /script/run_ueler.ipynb.
2. Select multiple channels.
3. Toggle one channel off and confirm it disappears from the viewer while the selection remains intact.
4. Toggle it back on and confirm previous rendering settings are preserved.

[yulewu]

Update Summary: Per-channel visibility toggles (commit b1140d8)

Added per-channel visibility checkboxes in the channel controls so users can temporarily hide channels without altering the underlying selection.

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Actions Taken

• Channel visibility UI:
  Added a per-channel visibility checkbox registry and rendered each channel row with a checkbox alongside the color dropdown.
• Rendering filter:
  Filtered the displayed channels by checkbox state so toggles hide/show channels immediately without touching selection or palette settings.
• Lifecycle cleanup:
  Cleared visibility controls when channels disappear on FOV changes to keep widget state consistent.

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Files Changed

• ueler/viewer/ui_components.py — added channel visibility control registry.
• ueler/viewer/main_viewer.py — rendered visibility checkboxes and filtered visible channels during display updates.
• dev_note/issue_tracking/issue66_channel_visibility.md — captured the implementation plan.

---

Tests

python -m unittest tests/test_rendering.py

• ✅ All tests passed

[yulewu]

Likely a layout/space issue: the per-channel checkbox exists in update_controls() but the Dropdown expands (and its long description=f"Color {channel}" takes width), which can squeeze the checkbox out of view.

Suggested minimal fix: shrink the color dropdown (and ideally remove/zero its description) so there’s guaranteed space for the checkbox.

Patch sketch (in ueler/viewer/main_viewer.py, ImageMaskViewer.update_controls)
Apply both to newly-created AND reused dropdown widgets:

if channel in self.ui_component.color_controls:
    color_dropdown = self.ui_component.color_controls[channel]
    # Ensure existing widget gets new sizing too
    color_dropdown.description = ""
    color_dropdown.style = {'description_width': '0px'}
    color_dropdown.layout = Layout(width='140px', min_width='140px', flex='0 0 140px')
else:
    color_dropdown = Dropdown(
        options=list(self.predefined_colors.keys()),
        value="Red",
        description="",
        disabled=False,
        layout=Layout(width='140px', min_width='140px', flex='0 0 140px'),
        style={'description_width': '0px'},
    )
    color_dropdown.observe(lambda change, ch=channel: self.update_display(self.current_downsample_factor), names='value')
    self.ui_component.color_controls[channel] = color_dropdown

(Checkbox is already Layout(width='20px'); this change should make it reliably visible.)

Validation
Restart kernel, re-run /script/run_ueler.ipynb, select multiple channels, confirm checkbox square is visible immediately left of each color dropdown and toggling hides/shows channel without changing selection.