diff --git a/docs/gui.rst b/docs/gui.rst index 7386b360..e1a2c931 100644 --- a/docs/gui.rst +++ b/docs/gui.rst @@ -48,17 +48,32 @@ Main GUI mouse controls (works in all views): - Start draw mask = right-click - End draw mask = right-click, or return to circle at beginning +Drawing masks +~~~~~~~~~~~~~~~~~~~~~~ + +Masks are started with right-click, then hover your mouse (do not hold it down), +and return it to the red circle to complete the mask. The mask should now be completed. + Overlaps in masks are NOT allowed. If you draw a mask on top of another mask, it is cropped so that it doesn't overlap with the old mask. Masks in 2D should be single strokes (if *single_stroke* is checked). If you want to draw masks in 3D, then you can turn *single_stroke* option off and draw a stroke on each plane with the cell and then press -ENTER. +ENTER. You can also draw multiple strokes on the same plane for +complex cell shapes, but do not do this in 2D if you plan to train a cellpose model +(the cell flows will not work correctly). .. note:: 3D labelling will fill in unlabelled z-planes so that you do not - have to densely label, for example you can skip some planes. + have to densely label, for example you can skip some planes, and the + cell will be interpolated between planes. + +After each mask is drawn in 2D, it is saved to the ``_seg.npy``. If this is slow (for +large images), this "autosave" option can be turned off in the "File" menu +("Disable autosave _seg.npy file"). In 3D, +the mask is never auto-saved, instead save masks by clicking CTRL+S, or "Save" in the +"File" menu. Segmentation options