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EPySeg is a package for segmenting 2D epithelial tissues. EPySeg also ships with a graphical user interface that allows for building, training and running deep learning models.

Training can be done with or without data augmentation (2D-xy and 3D-xyz data augmentation are supported). EPySeg relies on the segmentation_models library. EPySeg source code is available here. Cloud version available here.

ELEPHANT is a platform for 3D cell tracking, based on incremental and interactive deep learning.
It implements a client-server architecture. The server is built as a web application that serves deep learning-based algorithms. The client application is implemented by extending Mastodon, providing a user interface for annotation, proofreading and visualization.

The Binary Pattern Dictionary Learning (BPDL) package is suitable for image analysis on a set/sequence of images to determine an atlas of a compact region. In particular, the application can be maping gene activation accross many samples, brain activations in a time domain, etc.