![]() Currently, 40 open source imaging software projects, termed ‘Community Partners’, use the Forum as their primary interaction with users. The two software projects joined forces to build the Scientific Community Image Forum ( ) ( Rueden et al., 2019), an online resource for the worldwide scientific community to learn about image analysis from each other. For example, the teams advocate together for open source technologies, usability, and interoperability ( Carpenter et al., 2012 Kamentsky et al., 2011). The ImageJ and CellProfiler teams have worked together for many years, not just on mutually useful software development, but also in developing the bioimage analysis community into its healthy and cooperative state today. The projects also differ in their respective languages, with ImageJ being Java-based and CellProfiler Python-based. With over 10,000 publications to date, CellProfiler’s strength is in project-building, where complex pipelines of individual modules can be built to automate the processing of large experiments of images ( Carpenter et al., 2006 Kamentsky et al., 2011 McQuin et al., 2018). Cited in over 10,000 publications per year, ImageJ, as well as its plugins-included distribution known as Fiji, enable in-depth image investigations both are ideally suited for interactive, single-image processing and are popular choices for both novice and experienced developers alike to add functionality ( Schneider et al., 2012 Rueden et al., 2017 Schindelin et al., 2012). Over the years, both projects have developed independently, cementing themselves in the field of image analysis. ImageJ and CellProfiler are two of the most widely used open source image analysis platforms in science. ImageJ and CellProfiler are both committed to interoperability between their platforms with ongoing development to improve how both are leveraged from the other. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. No single platform can provide all the key and most efficient functionality needed for all studies. ![]() Here we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for 1) studying cell morphology and migration via tracking and 2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. Although many image analysis problems can be well-solved with one or the other, using these two platforms together in a single workflow can be powerful. ImageJ’s traditional strength is in single image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. ImageJ and CellProfiler have long been leading open source platforms in the field of bioimage analysis.
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