Macro programming for everyone!
JIPipe is a free and open source visual programming language built on ImageJ that allows you to create fully automated image analysis pipelines by just drawing a flow chart!
What can JIPipe do for you?
Reproducibility without programming
Design image analysis workflows without the need for programming
JIPipe is a visual programming language, meaning that you just need to design a flowchart of the image processing steps. Save the project, re-open it on another computer, and re-run it whenever you want!
Built on Fiji/ImageJ
Re-use your existing ImageJ knowledge
JIPipe provides not only its own features, but integrates a multitude of existing commands and features. This includes the execution of ImageJ macros.
Cellpose/Omnipose/TesseractOCR
Utilize AI without effort
JIPipe automatically takes care of setting up non-ImageJ tools, including Cellpose, Omnipose, TesseractOCR, TSOAX, and more!
OMERO support
Connect to OMERO repositories
Use JIPipe to work with images and metadata in OMERO repositories, and upload your results.
Exclusive filament processing tools
Utilize our powerful filament operations library
JIPipe ships with its custom 3D filament/graph toolbox that helps you with processing neurites, hyphae, surface structures, and more
Python and R support
Script with Python and R
JIPipe allows you to integrate R, Python, and ImageJ macro code in your pipeline.