@@ -109,4 +109,23 @@ Note that this action will be applied to all the time frames of the movie, and c
For example, the tracks must not have frame gaps (missing one frame). If that happens, the `sanity check` option will detect it and fix it by splitting the gap in two different gaps.
If some napari layers had been wrongly closed, this step will also re-open them.
It also checks if the labels seemed ok or if something is weird.
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It also checks if the labels seemed ok or if something is weird.
# Group cells options
**Allows to create group of cells (classify them).** Cells can be manually assigned to a cell group by clicking on them. This is useful to distinguish different type of cells visually or/and in the analysis in the Outputs options.
`Group name` allows to choose the name to give to a new Group of cells, or to assign a cell to the current `Group name` group.
A cell can be assigned to the current group by holding <kbd>Shift+Left click</kbd> on the cell.
<kbd>Shift+Right click</kbd> will remove the cell under the cursor from its current group, and set it as unassigned.
`Show groups` will add a `Groups` layer in Napari, in which the cell are colored by the group they are in. Cells that are not in any group are black.
`Reset groups` remove all created groups. All cells are not in any groups.
`Cells inside ROI to group`: assign all the cells that are inside the currently selected ROI in the current frame (in the `ROIs` layer) to the current group (set by `Group name`). Cells that are assigned to a group are assigned all along the track (in all frames where this cell is present).
When the segmentation is saved by clicking on <kbd>s</kbd> when the `Segmentation` layer is active, the group information is also saved, in the EpiCure data file (file in the `epics` folder that ends with `_epidata.pkl`. When the movie is reopened in EpiCure, it will be automatically reloaded.
