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PanSeg Interactive - Napari

Technical Issues

The renaming process is ongoing, and you might encounter technical issues The new conda-forge package is not yet released, until then the in-app update does not work. Issues with the windows installer have been resolved.
If you encounter issues, please use PlantSeg <= 2.0.0rc14 for now, thank you!

Interactively apply operations to your images and run the segmentation pipeline using the GUI of PanSeg. PanSeg uses napari as its front-end.

Start PanSeg according to your chosen installation method. From the terminal, you can start PanSeg in the GUI mode with:

panseg --napari
or
panseg -n

PanSeg 2.0 interface

Parts of the GUI

Top left: Settings

  • Change your tool (pan, brush, boxselect, ...)
  • Change look of image (opacity, label colors,..)
  • Change tool settings (brush color & size, select shape)

Bottom left: Layer selection

Your loaded layers get displayed here. Toggle their visibility with the eye icon. Below, you can switch to a grid view or a 3D view with the respective icons.

Right: PanSeg

This is the main interface of PanSeg. On the bottom you can switch through the different sections of PanSeg.

Hotkeys

General

  • Ctrl+i Increase font size
  • Ctrl+o Decrease font size
  • Ctrl+w Quit PanSeg

Proofreading

  • n Merge/Split using current scribbles
  • j Clean scribbles