@@ -168,6 +168,22 @@ A cell can be assigned to the current group with :round_pushpin: **<kbd>Shift+Le
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.
## Automatic cell group assignement
Options are proposed to automatically assign several cells into one group, based on intensity measurement.
To set this option, click on the `Group from track intensity...` button in the `Group options` panel.
It opens-up an interface that allows to choose the criteria for the cell classification.
The positive cells based on the selected criteria will be assigned to the current group name that can be set in the `Group name` parameter in the main interface.
Choose the layer to use for the classification: the intensity in this layer will be measured in each cell. The layer can be a non EpiCure-layer . It only have to be opened in the same Napari and put at the same scale.
For example it can be a probability map that are calculated by [DeXtrusion](https://gitlab.pasteur.fr/gletort/dextrusion). In the notebook [EpiCure_DeXtrusion_Interaction.ipynb](https://gitlab.pasteur.fr/gletort/epicure/-/blob/main/notebooks/EpiCure_DeXtrusion_Interaction.ipynb?ref_type=heads) in this repository, dextrusion probability maps are overlayed with the EpiCure data and used to automatically classify SOP cells if they have been detected by DeXtrusion.
For each track, the intensity will be measured in all the pixels of the cell at each time frame. You can choose whether you want to measure the mean value of these intensities, or the sum/max/min/median. Then fix a threshold to consider the track as positive if the measured value is above this threshold.
