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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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* [Cleaning options](#cleaning-options)
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* [Group cells options](#group-cells-options)
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# Edit segmentation on single time frame
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`EpiCure` proposes features to ease the manual segmentation correction on single time frame (the current one), through several [shortcuts](#shortcuts) and special [features](#features).
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## Shortcuts
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The segmented cells are represented as label. There are several possibility for label edition in `Napari` + extra features from `EpiCure`.
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EpiCure shortcuts are linked to the `Segmentation` layer, so it should be selected for the shortcuts to work.
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### General options
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* Press <kbd>s</kbd> to save the current state of the segmentation. The file will be saved in the output folder, named `**imagename**_labels.tif` and can be reloaded later.
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* **Press <kbd>h</kbd> to show/hide the main `EpiCure` shortcuts** list.
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### Visualization :eye: shortcuts:
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* The labels (cells) can be displayed as filled areas (put `contour` to 0) or only the contour lines can be shown with the `contour` option.
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* To see only the current label (the pixels which have the value that is currently active in the `label` field), check the `show selected` box on the left panel.
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* Click on the eye icon next to the `Movie` layer to show/hide it.
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Shortcut: **press <kbd>v</kbd> to show/hide the movie** (visible).
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* Click on the eye icon next to the `Segmentation` layer to show/hide it.
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Shortcut: _press <kbd>b</kbd> to show/hide the segmentation_ (binary).
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* **Press <kbd>5</kbd> to switch to zoom/moving mode**.
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* **Press <kbd>g</kbd> to see only the movie layer**.
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### Segmentation editing: corrections :wrench:
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* You can merge two neighboring cells that were wrongly segmented as 2 instead of one cell. `EpiCure` will relabel one of these two cell with the other cell label, and performs a morphological closing to bring them together if they are not touching. _Note that if there is another cell is between, they cannot be merged; you will get two cells with the same label._
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**Press <kbd>Control</kbd> + <kbd>left-click</kbd> to merge 2 cells**, starting from inside the first cell until the second cell with the mouse button clicked.
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* You can also split one cell that was wrongly segmented as one into the two correct separated cells. `Epicure` will do a watershed separation to find the limits of the two cells.
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**Press <kbd>Control</kbd> + <kbd>right-click</kbd> across the junction to split the cell**, starting from the middle of the first cell, until the middle of the second cell with the mouse button clicked. The program uses the first point of the dragged-click as a seed for the first cell, and the last point of the dragged-click as the second seed. If it fails, changing the starting and final points can improve the separation.
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* A cell can also be split by drawing the junction (usefull when intensities are very messy making watershed separation to fail). **Press <kbd>Alt</kbd> + <kbd>right-click</kbd> and draw the junction**, keeping the right button clicked all along. The plugin will then split the cell in 2, one with the previous value and the new one with the maximum label + 1 value. If your line drawing spread over the neighbor cells, it will not affect them.
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### Segmentation editing: drawing :paintbrush:
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* Press <kbd>2</kbd> to switch to drawing mode or click on the pencil icon. You can draw a label with this pencil tool. When it is selected, it will draw with the current value in the field below. You can choose the precision of your drawing with the `brush stroke` parameter (the brush size can be decreased with <kbd>[</kbd> and increased with <kbd>]</kbd>.
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* **Press <kbd>3</kbd> to switch to fill mode**.
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To replace a whole label by a new value (label), you can use the `fill` option. Put the desired value in the label field and click on the label to fill with it.
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* To select a label, you can put the value in the `label` field or you can use the picker tool and click on the corresponding area. **Press <kbd>4</kbd> to switch to picker mode**.
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* To delete a label, put `0` as the current value (_or press <kbd>1</kbd>_), select the `fill` tool and click on the label to remove. **Or <kbd>right-click</kbd> on a label to erase it directly**.
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* To draw a new cell, you have to select a value that is **not used yet** in all the movie. The simpler is to use the maximal current value and add one to be sure to use a new value. You can **get this value by pressing <kbd>m</kbd>**. It will directly put the max value + 1 in the active label field and active the drawing mode.
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* The `preserve labels` option allows you to freeze other labels than the current active one. If you try to draw on top of another label, it will not work as the other labels have been locked. This is convenient when you draw a new label to be sure to draw the new cell just against the other ones without modifying them. If you try to draw on a label when this option is activated, you will get an error message appearing.
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Complete list of Napari label layer shortcuts (From File>Preferences>Shortcuts):
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## Features
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Several features are proposed:
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* [Check Map](https://gitlab.pasteur.fr/gletort/epicure/-/wikis/Check-Map) to note the cells that are correctly segmented and already verified :white_check_mark:.
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* [Suspect outliers](https://gitlab.pasteur.fr/gletort/epicure/-/wikis/Outliers) determine cells suspicious of having an error, based on a few morphological features :mag:
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* [Seeds](https://gitlab.pasteur.fr/gletort/epicure/-/wikis/Seeds) to perform a watershed segmentation from several placed seed points.:heavy_division_sign:
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<br>
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---
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---
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# Edit segmentation on several time frames
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## Manual tracking edition
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Press <kbd>t</kbd> to go into manual tracking mode (a message should appear when you enter this mode).
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<kbd>Left-click</kbd> on the cell to track from the beginning of its track to its end.
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The first <kbd>left-click</kbd> that you do would determine the id of the track to edit (the cell value that you clicked), and the movie will go to the next frame.
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Then, for each <kbd>left-click</kbd>, the cell below the cursor will be set to this track id value and the movie will move to the next frame.
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To finish the track editing, <kbd>right-click</kbd> and a confirmation message will appear. If you reach the end of the movie and do one more <kbd>left-clik</kbd>, the manual tracking mode will also be stopped.
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---
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# Cleaning options
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Options to ensure clean and correct EpiCure files.
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## Remove border cells
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Remove all segmented cells that touch the spatial borders of the image. This parameter allows to get rid of cells that are partially outside of the imaged region and thus not complete.
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The parameter `Border width` allows to extend the requirement for the cells to be considered as fully inside. Cells that have at least one pixel at a distance less than `Border width` pixels from the image limits will be removed.
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Note that this action will be applied to all the time frames of the movie, and cannot be cancelled (if you wish to cancel it, you then need to restart EpiCure without saving the files).
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