Start EpiCure

Start EpiCure: load the movies and metadata

Choose Start epicure in Napari Plugins>Epicure to open it.

EpiCure handles several inputs format through the bioio module. However, if some format is not correctly recongized/handled by EpiCure, you can open the images in Napari with any other plugin (for example napari-bioformats, napari-aicsimageio) and use the Start from open layers option (see more here).

Loading the movies

In the Start EpiCure step, you have a dedicated interface in the right part of the main interface.

The first file to choose is the movie containing the epithelial staining, with the image file parameter. It should be 2D(+time/channels) file. 3D is not handled. If a file has a Z dimension and no temporal dimension, EpiCure will swap them and use the Z axis as time.

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 (it should only contain the segmentation), to select with the segmentation file parameter. 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.

If the input movie file had already been processed with EpiCure previously (and saved), EpiCure will automatically propose to load the saved file and reload the previous parameters. You can directly click START CURE in this case.

Movie metadata

The information of pixel size in xy dimensions and of temporal resolution can be set with the scaling parameters: scale xy (the size of one pixel in the corresponding unit), unit_xy (which unit, usually µm), timeframe (the temporal resolution at which the movie is acquired) and unit_t (which unit for the temporal resolution).

These scaling information is then used to display the movie with the correct sizes and export the measures in scaled units if the option is selected.

Since version 1.3 of EpiCure, files are loaded with the bioio python library, to support several formats. EpiCure reads the metadata of the input file with this library and fill the value of the scaling parameters of the interface. Depending on python/module versions and the input file itself, all the information might not be correctly extracted, so we recommend to check these values to be sure that the movie will be properly scaled in EpiCure.

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.

show scale bar will display a scale bar overlaid on the movie. This can also be manually set by going in Napari>View>Scale Bar>Scale Bar Visible.

allow gaps: allows tracks to have a few gaps (intermediate frames in which one label is not present, but reappear later).

epithelial cells: EpiCure has been developed and optimized for epithelia movies, with jointive cells. However, you can still use it for non jointive cells by unselecting this option. Note that some options might not be usable in that case

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.

Using EpiCure without interface

While EpiCure is optimized for a graphical usage as its scope relies on easing manual edition of segmentation, there's a possbility to launch it without starting Napari first (or at all). This can be useful for automatic testing or batching some process. See our released notebooks for example of usage or our test files.

Start from opened layers

To make EpiCure compatible with as many input formats as possible, we added the option to start it from already opened layers, so that the images can be opened with other readers than the one proposed in EpiCure if necessary.

Both the raw image and the segmentation can be opened before to start EpiCure, or only the raw image.

In Plugins>EpiCure, choose the option Start from opened layers.

In the parameters interface that open on the right side of the viewer, select the layer that corresponds to your raw movie (the layer containing the junction staining) in the movie parameter.

Select the raw file of the movie in the movie path parameter. This will not open it as it is already opened, but is necessary to know the path and name of the image to save correspondingly the output files.

Select the layer containing the segmentation in the segmentation parameter if you have one, or select None otherwise.

Once the parameters are properly filled, click Use selected layers and you will be back to the "normal" EpiCure starting interface to check the image metadata and choose the main parameters of your analysis.