@@ -110,3 +110,22 @@ Note that this action will be applied to all the time frames of the movie, and c
...
@@ -110,3 +110,22 @@ 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.
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.
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.
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.
