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Welcome to EpiTools!#

EpiTools is a Python package and associated napari plugin to extract the membrane signal from epithelial tissues and analyze it with the aid of computer vision.

The development of EpiTools was inspired by the challenges in analyzing time-lapses of growing Drosophila imaginal discs.

The folded morphology, the very small apical cell surfaces and the long time series required a new automated cell recognition to accurately study growth dynamics.


First, install napari.

The recommended way to install EpiTools is via pip

python -m pip install epitools

To install the latest development version of EpiTools clone this repository and run

python -m pip install -e .

If working on Apple Silicon make sure to also install the following package from conda-forge.

conda install -c conda-forge pyqt


If you encounter any problems, please file an issue along with a detailed description.


Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

Napari plugin#

When you install EpiTools, both napari and the EpiTools plugin will also be installed. See Using the EpiTools plugin for napari for guidance on using the plugin.

Python API#

See the Python API pages for the full API of the analysis modules in EpiTools. EpiTools currently contains to following analysis modules: