Services
JIPipe
JIPipe is a free and open source visual programming language also for non-programmers built on ImageJ that allows the creation of fully automated image analysis pipelines by just drawing a flow chart.
Who is the service recommended for?
- Life scientists
- Microscopy facility staff
- Bioimage analysts
- Trainers in bioimage analysis
Which infrastructure do you need?
- Download and installation of JIPipe (no license required)
Which expertise do you need?
- Basic concepts of bioimage analysis workflows (required). Explore the bioimage analysis material collection of the NFDI4BIOIMAGE Training Hub
- expertise in ImageJ (recommended). Explore the ImageJ collection of the NFDI4BIOIMAGE Training Hub
What is JIPipe and how can you benefit from it?
JIPipe is a visual programming language, meaning that it allows you to program your avanced own image/ data analysis workflows but without involving any (or only minimal in certain cases) writing of text-based scripts. The main goal is to allow you to create reproducible workflows, even if you are not a programmer. Learn more here.
JIPipe is a workflow language designed for batch processing and thus implements a variety of features. These are designed to make batch processing convenient to implement while ensuring maximum flexibility. Learn more here.
JIPipe allows the integration of a variety of ImageJ- and non-ImageJ tools. It automatically takes care of setting up cellpose, Omnipose, python, R, ilastik, napari, and many other packages in a reproducible way. JIPipe also guides you through the export of your pipeline as workflow RO-Crate, simplifying the publication of FAIR Data Objects.
JIPipe can further access images from OMERO repositories for analysis and add results of the analyses. Learn more here.
How to get started:
If you want to use and learn more about JIPipe , get started with its installation, explained by Ruman Gerst in this video tutorial. Follow further tutorials and use the documentation to learn about available image analysis workflows and to create your own.
Read more about the benefits of JIPipe, available analysis workflows, python and R support or explore tutorials on the JIPipe website.
Check out a series of JIPipe tutorials or follow an entire course of basic and advance usage of JIPipe with online material here.
Learn how to access bioimages from an OMERO instance using JIPipe or sneak into the documentation.
