Biologists often need to use a variety of different software to acquire and analyze data and connectivity between these tools can be crucial. Due to the Mac-only support of NIH image and its pioneering status there were few early examples of NIH Image connecting with external programs. There were several prominent examples mediated by export of an open file format however, such as the export of a .csv file for statistical analysis. From the beginning of ImageJ there was interest in directly connecting to external toolkits without the need for exporting and opening files and early connections to MATLAB (MathWorks Inc.) are a prime example. ImageJ’s third party tool connections have allowed it to be used in image workflows and take advantage of algorithmic strengths provided by MATLAB. ImageJ connectivity with other software programs, such as Imaris, Cell Profiler5 and Knime6–8, have also been established. While these collaborations were not specifically envisioned by Rasband when designing the program, they enable a variety of new functionality ranging from automated screening and segmentation-based measurements to sophisticated signal processing analysis, thus further extending the utility of ImageJ.
