ImageJ is an open source Java image processing and analysis library used extensively in biomedical sciences. Active Segmentation is a plugin providing user interface to scientists, allowing them to use Machine Learning algorithms for segmentation and classification tasks. The aim of the Active Segmentation is to provide researchers an extensible toolbox enabling them to select custom filters and machine learning algorithms for their research. Moreover, it provides the support for scientists without strictly technical background (does not require programming skills to apply above mentioned tools). The idea behind this project is to extend active segmentation with modern deep learning methods for image analysis using Deeplearning4j library.