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* [Edit segmentation on single time frame](#edit-segmentation-on-single-time-frame)
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* [Edit segmentation on several time frames](#edit-segmentation-on-several-time-frames)
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* [Edit segmentation on several time frames](#edit-segmentation-on-several-time-frames): tracks edit mode.
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* [Cleaning options](#cleaning-options): general cleaning/checking of the segmentation and EpiCure files to ensure.
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* [Group cells options](#group-cells-options): classify cells into group (type) of cells.
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* [ROI options](#roi-options): apply some process to only some drawn region.
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... | ... | @@ -54,12 +54,33 @@ Complete list of Napari label layer shortcuts (From File>Preferences>Shortcuts): |
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# Edit segmentation on several time frames
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## Merge tracks temporally
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To correct tracks, :round_pushpin: **press <kbd>t</kbd> to active the tracks editing mode.**.
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To link two cells that have not been correctly tracked as one, :round_pushpin: **press <kbd>e</kbd> to activate the temporally merge mode**. **Click left** on the cell that should be the last one of its track. EpiCure will directly move to the next frame. **Click right** on the corresponding cell. The two tracks will be merged as one.
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:warning: The other shortcuts are not active anymore in this mode, only the shortcuts listed below. To leave this mode and reactive the usual shortcuts, either finish your edit or press <kbd>t</kbd> again.
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## Merge two tracks
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:round_pushpin: **Press <kbd>t</kbd> to go into track edit mode** (a message should appear when you enter this mode).
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To link two cells that have not been correctly tracked as one (temporal merge) or that have been wrongly splitted in two in the segmentation in several frames (spatial merge), :round_pushpin: **Click left** on the first cell to merge. **Click right** on the second cell to merge. The two tracks (for temporal merging) or the two cells (for spatial merging) will be merged as one.
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### Temporal merging
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If the two cells clicked are not in the same frame, you are merging two tracks temporally.
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If you select cells that are not the last or first one of their tracks, or if the two clicked cells are not in consecutive frames, EpiCure will refuse to merge them and quit the track merging mode.
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If the clicks are correct, the two tracks will be fused in one longer track with the first cell label.
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### Spatial merging
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If the two cells clicked are on the same frame, you are merging two cells spatially as one (correcting a splitted segmentation).
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This will create a new track containing the two merged segmentation as one cell. The merge of the cells will be done from the current frame and until one of the two cells is not present anymore.
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## Split temporally track
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:round_pushpin: **Press <kbd>t</kbd> to go into track edit mode** (a message should appear when you enter this mode).
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:round_pushpin: **Press <kbd>Control+Right click</kbd> to split a track**.
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The track under the click will be splitted in two tracks: a new track will be created from the current frame until the last frame of the initial track. The frames of the initial track previous to the clicked frame will be untouched.
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## Manual tracking edition
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... | ... | |