Panels description

Panels

para_panels

1. Layer controls

This is a default panel in napari viewer for viewing/editing a label layer (segmentation layer).

Here are some key features:

  • Picker mode: You can select a label by clicking it with mouse. Press L to change to this mode.
    • Pan/Zoom: You can hold space key and use left button/wheel of mouse to pan/zoom the image in Picker mode.
  • Eraser: You can set a pixel as non-cell region (set the value to 0) with the eraser tool. Press E to change to this tool.
  • Paint brush: You can paint a region with a specific label. Press P to change to this tool.
  • Shuffle colors: Two neighboring cells can occasionally be assigned the same color. To shuffle the colors, press this button (top leftmost).

2. Layer list

You can select a layer from segmentation, cell/non-cell image, raw image, etc., and can hide or change the opacity of them.

3. Tools for change the view point

The most import function here is the "home" function (rightmost), which allows you to resize the image to see the entire image.

4. Current layer/cursor position/selected label

This panel is not used in this module, but it is useful in Module 3D correction.

5. Canvas (Segmentation results)

The segmentation results and other reference images are shown here.

  • The slice number of the currently displayed one can be easily calculated using the information surrounding the slide bar.

    E.g, "Slice(1-50)" together with "12|49" indicate current slice number = 1 + 12 = 13.

6. States

Three types of information are shown here:

  1. The size of the 3D image.
  2. The largest cell ID in current segmentation result.
  3. The cached states that can be retrieved using undo/redo (By default, 10 steps in maximum).

7. Hotkeys information

The (default) hotkeys used in Seg2D+Link module.

8. Export

Export the 3D segmentation result.

9. State info

Show information of current state such like:

  • Performing operation xxx...;
  • Operation xxx was done;
  • Warning message: xxx;
  • etc.

IMPORTANT: To avoid software crashes, always ensure that the previous operation is finished before starting the next.d