JIPipe allows anyone to create advanced image and data processing pipeline without the need for learning a macro programming language. Just pick which functions should be applied and arrange them in a flow chart. All technical parts are handled automatically.

The image processing capabilities of JIPipe are built on established functionality provided by ImageJ/Fiji. You will find many familiar functions, but redesigned to make them easily adaptable into a batch processing workflow.

JIPipe does not only contain many features from ImageJ, but also enhanced versions of older commands that have more flexibility, support 5D images, and are more convenient to use inside an automated batch processing environment.

The software comes with a powerful library of data management functions that help you with automatically processing all your data in one go. Due to the high flexibility of the feature, you can rapidly adapt your analysis pipeline to any existing structure without the need for re-arranging the data itself to fit into a pre-defined organization. Metadata can be easily extracted from files, directories, OMERO, and other data sources.

JIPipe comes with advanced table and result processing features that allow to process and plot statistics without any external tools. If even more advanced features are needed, R and Python code can be directly run within JIPipe.

Our software comes with a powerful 5D filament and contour processing library that makes even advanced operations on filaments or graph-like structures easily accessible.

We integrated features from the 3D ImageJ Suite and the ImageJ 3D Viewer plugin that allow you to measure and visualize 3D structures.

JIPipe currently integrates Cellpose and Omnipose. We provide operations for applying existing models and training (fully or continued training) new models. Additionally, JIPipe can utilize other machine learning tools like Weka.

All results generated by JIPipe can be conveniently exported via the integrated automated exporter feature. Alternatively, the software provides powerful operations that export data to the hard drive or OMERO.