Usage

You can launch EpiCure in Napari by going to Plugins>epicure>Start. It will open an interface at the right side of the window where you can select the files to use.

The first file to choose is the movie containing the epithelial staining. It should be 2D(+time), .tif file. If the file contains several chanels, the plugin should detect it and show the junction_chanel parameter, to choose the chanel that contains the junction staining. The plugin will display only this chanel. If you wish to also see the other chanels, use the option show other chanels in the advanced parameters panel.

The second file is the segmentation of this movie (also a .tif file). It can be a binarized file of the junctions (skeletonized) or a labelled file (each cell is filled by a unique number). Note that if you haven't done the segmentation yet, there's an additional option in EpiCure to directly run EpySeg on the loaded movie.

Advanced parameters

output dirname is the name of directory where all files generated by EpiCure will be saved. By default, it is placed in the input movie directory and called epics.

show other chanels will display the other chanels of the original movie.

process frames parallel: if this is checked, some operations will be performed in parallel, processing multiple frames at the same time. The number of parallel threads run together is defined by the parameter nbparallel_threads, which is by default 75% of the computer's cpu numbers.

verbose level defines the amount of messages that are printed to the user. By default, some information or warning messages are shown. If this parameter is put to 0, very few messages will appear while if it's put to 3, a lot of information useful for debugging will be shown.

Start EpiCuring

When you have selected the two files, you can start editing by clicking on the Start cure button. It will open the two movies and open the interface that let you choose the steps to do:

• Edit: clean the segmentation or correct manually errors through EpiCure options 🔧
• Inspect: determine cells suspicious of having an error, based on a few morphological or track features, or handle cellular events as divisions 🔍
• Track: links the labels from one frame to another to reconstruct the whole cell track.
• Output: measure/display cell or track features, export results to other plugins/softwares 📤
• Display: display additional informations (segmentation skeleton, general informations...) or a spatial grid 🔍
• Preferences: to set-up user-specific preferences as keyboard shortcuts 🔠

General principle

In EpiCure, the segmented cells are represented as labels: each cell is assigned a unique number, that will be conserved in all time frames that the cell is present. All pixels belonging to the cell are assigned to its value. They are represented in EpiCure in a Napari Label layer called Segmentation.

Tracks displays the trajectory of each cell by marking its centroid at each time frame. The value of a track is the same as the cell label.

Inspect helps the user to correct the segmentation by flagging some cell that might be wrongly segmented or handling other cellular events as divisions.

EpiCure has several keyboard or mouse shortcuts to allow interactive corrections. EpiCure shortcuts are linked to the Segmentation layer, so it should be selected in Napari for the shortcuts to work.

Shortcut customisation

You can redefine EpiCure shortcuts to put your favorite keys instead of EpiCure default ones. For this, open the Preferences option in Napari>Plugins>EpiCure>Edit preferences. Choose the shortcuts to use and save them. See the Preferences page for more information.

:heavy_exclamation_mark: the new shortcut configuration will be active only at the next EpiCure session. If you already have an EpiCure opened, restart it to apply the new shortcuts.

General options

• Press s 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. Additional informations specific to EpiCure (cell groups, tracks graph (lineage), suspects) are saved at the same time, in a file named **imagename**_epidata.pkl. When the EpiCure files are re-opened, this file will be reloaded.

• Press h to show/hide the main EpiCure shortcuts list. Press it several times to go through the different shortcut lists.

• Press a to open a new op-up window that list ALL the EpiCure shortcuts.

• Press Shift-s to save screenshots of the whole movie, with the current display.

Visualization 👁 shortcuts:

• 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. Shortcut: Ctrl-c or Ctrl-d to increase (or decrease) the contour size.
• 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.
• Click on the eye icon next to the Movie layer to show/hide it. Shortcut: press v to show/hide the movie (visible).
• Click on the eye icon next to the Segmentation layer to show/hide it. Shortcut: press b to show/hide the segmentation (binary).
• Press 5 to switch to zoom/moving mode.
• Press c to see only the movie layer.
• Press g to show/hide a grid to have a spatial repere. See Display documentation for more details.

Additional options

Concatenate EpiCured movies

Concatenate temporally two EpiCured movies: to treat a huge movie, it can be convenient to split it temporally in two (or more movies). You can then correct each movie with EpiCure, and recombine it with this option.

Segment with EpySeg

When starting EpiCure, once you have selected the movie to process and the junction channel, you have to load the file containing the segmentation of the epithelia movie. If you haven't done it yet, you can use the Segment now with EpySeg button that appears in the Start EpiCure interface. This option uses the napari-epyseg plugin to directly run EpySeg on the movie. It will run with the default parameters. If you want to change some parameters, either use directly the napari-epyseg plugin within Napari (limited number of options) or use the original distribution of EpySeg (you can launch it with python -m epyseg in your python environement).

Note that the option requires to install the napari-epyseg plugin which is not installed by default in the EpiCure release. You can install it by typing pip install napari-epyseg in the environement or by going to Plugins>Install\Uninstall Plugins in Napari interface.