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    • Update Edit authored by Gaëlle LETORT's avatar Gaëlle LETORT
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    ......@@ -17,27 +17,27 @@ General shortcuts are documented [here](https://gitlab.pasteur.fr/gletort/epicur
    ### Segmentation editing: corrections :wrench:
    * 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._
    **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.
    :round_pushpin: **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.
    * 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.
    **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.
    :round_pushpin: **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.
    * 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.
    * A cell can also be split by drawing the junction (usefull when intensities are very messy making watershed separation to fail). :round_pushpin: **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.
    ![mergecells](uploads/268878843401755a144e6469a9e2fd17/mergecells.png)
    ### Segmentation editing: drawing :paintbrush:
    * 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>.
    * :round_pushpin: **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>.
    * **Press <kbd>3</kbd> to switch to fill mode**.
    * :round_pushpin: **Press <kbd>3</kbd> to switch to fill mode**.
    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.
    * 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**.
    * 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. :round_pushpin: **Press <kbd>4</kbd> to switch to picker mode**.
    * 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**.
    * 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. :round_pushpin: **Or <kbd>right-click</kbd> on a label to erase it directly**.
    * 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.
    * 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. :round_pushpin: 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.
    * 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.
    ......@@ -56,13 +56,13 @@ Complete list of Napari label layer shortcuts (From File>Preferences>Shortcuts):
    ## Manual tracking edition
    Press <kbd>t</kbd> to go into manual tracking mode (a message should appear when you enter this mode).
    <kbd>Left-click</kbd> on the cell to track from the beginning of its track to its end.
    :round_pushpin: **Press <kbd>t</kbd> to go into manual tracking mode** (a message should appear when you enter this mode).
    **<kbd>Left-click</kbd> on the cell to track** from the beginning of its track to its end.
    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.
    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.
    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.
    **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.
    ---
    ---
    ......@@ -96,8 +96,8 @@ It also checks if the labels seemed ok or if something is weird.
    `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.
    A cell can be assigned to the current group with :round_pushpin: **<kbd>Shift+Left click</kbd> on the cell**.
    :round_pushpin: **<kbd>Shift+Right click</kbd> removes 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.
    ......@@ -107,7 +107,7 @@ A cell can be assigned to the current group by holding <kbd>Shift+Left click</kb
    ![group-ui](uploads/bc7efcc62c0b8b64b96500f4a2f3f17a/group-ui.png)
    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.
    When the segmentation is :round_pushpin: **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.
    ---
    ......@@ -140,7 +140,7 @@ If no shape is selected, but there is exactly one shape in the `Drawings` layer,
    To place/add seeds, you can either check the `Seed options` parameter in the `Edit` panel, press `create seeds layer` if it's not there yet and select the `+` button in the top left panel to add points.
    _Shortcut_: You can directly press <kbd>e</kbd> when the `Segmentation` layer is active, and each <kbd>left-click</kbd> will place a new seed if there is no cell below. <kbd> right-click</kbd> to stop adding seeds.
    :round_pushpin: _Shortcut_: You can directly press <kbd>e</kbd> when the `Segmentation` layer is active, and each <kbd>left-click</kbd> will place a new seed if there is no cell below. <kbd> right-click</kbd> to stop adding seeds.
    ## Automatic positioning of seeds from previous time point
    ......