FOCUS ON BIOIMAGE INFORMATICS HISTORICAL COMMENTARY NIH Image to ImageJ: 25 years of image analysis Caroline A Schneider, Wayne S Rasband & Kevin W Eliceiri For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects. The last 50 years have seen tremendous Given the great success and impact Maryland graduate program that would technological advances, few greater of ImageJ, one would expect that this allow him to pursue his master’s degree than in the area of scientific computing. application was a software initiative with in computer science and thus leave the One of the fields in which scientific official backing and formal planning by a service early. One day in 1970, in the computing has made particular inroads central funding body. Despite its original commons at the University of Maryland, has been the area of biological imaging. name, NIH Image, and its home at the US College Park, he saw a notice for a part- The modern computer coupled to National Institutes of Health (NIH) for time programming position at the NIH in advances in microscopy technology is over 30 years in some form, ImageJ is a Bethesda, Maryland, USA, to work on the enabling previously inaccessible realms product of need, user-driven development laboratory instrument computer (LINC) in biology to be visualized. Although the and collaboration—rather than a specific created at the Massachusetts Institute roles of optical technologies and methods plan by the NIH to create it at the onset. of Technology. Rasband applied for this have been well documented, the role ImageJ became what it is through years position, was hired and worked at the NIH of scientific imaging software and its of collaborative effort, and NIH nurtured until he retired in 2010. origins have been seldom discussed in any it by providing the resources to support historical context. This is due in part to the the primary programmer, Wayne Rasband, NIH Image: image analysis on the Mac relative youth of the field, the wide variety throughout this period. In this current When Rasband began working at the of imaging software tools available, sheer age of careful oversight and scrutiny from Research Services Branch at the National © 2012 Nature America, Inc. All rights reserved. America, Inc. © 2012 Nature diversity of subfields and specialized tools, administrative bodies, the story of ImageJ Institute of Mental Health, part of the and the constant creation and evolution of and the independent track that Rasband intramural campus of the NIH, most new tools. had in its development is both interesting scientific data processing was done on npg In this great diversity and change, one and telling for other projects. To best mainframe computers, and the personal software tool has not only survived but understand this, one needs to look at how computer revolution was just beginning. thrived. The scientific image-analysis pro- ImageJ started. There was no image-analysis program for gram, ImageJ1,2, known in previous incar- Rasband created NIH Image, the the Macintosh computer, and Rasband nations as NIH Image3, was an early pio- predecessor to ImageJ, at the NIH in had just obtained one of the first Apple neer in image analysis. Twenty-five years 1987, but the foundation for this program Macintosh (Mac) II computers. Rasband after its introduction the program not only was laid even earlier at the beginning realized that it had the appropriate persists but continues to push and drive of Rasband’s career. Rasband received hardware and low-level software to be the field. It does so not by continuously his bachelor’s degree in math from the an ideal base for a small, low-cost image- reinventing itself but by sticking to a core University of New Mexico, Albuquerque, analysis system; all it needed was some set of design principles that have allowed in 1965. He was involved early on with software for image analysis. Rasband it to become a modern image-processing the IBM computer punch card systems decided to write that software in support platform and yet retain an interface that a while still in school. He leveraged this of the imaging analysis needs he saw at the user from over 20 years ago would recog- expertise to get a job with the State of time: chiefly, better access in terms both of nize and readily use. New Mexico’s Department of Automated ease of adoption and cost. Processing, where he performed It was his goal to have a low-cost Caroline A. Schneider and Kevin W. Eliceiri are common business-oriented language image-analysis system that the average at the Laboratory for Optical and Computational (COBOL) programming and general bench scientist could afford and deploy. Instrumentation, University of Wisconsin at Madison, systems programming. Shortly thereafter, Rasband wanted to create a system that Madison, Wisconsin, USA. Wayne S. Rasband is at the Rasband was drafted by the US Army and was smaller and more affordable than Section on Instrumentation, US National Institutes of Health, Bethesda, Maryland, USA. assigned to the Pentagon. While there, his earlier software systems that required e-mail: [email protected] Rasband became aware of a University of the $150,000 PDP-11 minicomputers NATURE METHODS | VOL.9 NO.7 | JULY 2012 | 671 HISTORICAL COMMENTARY FOCUS ON BIOIMAGE INFORMATICS in use at the time. He had developed an were some of the first users of the program beyond the Mac platform. The late 1990s image-analysis program called “Image” because autoradiographs, computed was a notable period in Apple history for this platform. The program ran an axial tomography or positron emission as the Mac was in a period of decline, imaging system that used a rotating drum tomography scans and X-rays could be with the PC rapidly gaining ground. In film scanner to digitize images and a viewed, analyzed and notated. As NIH scientific research, the Mac still had a 512 × 512 pixel frame buffer to display Image became increasingly used in many loyal following, but this following, too, was the digitized images, and it supported a fields—biological microscopy being the being eroded both owing to technologies custom-built joystick that could be used to largest—the functionality of the program only being available on the PC platform outline objects. The PDP-11 systems were and application base grew. and the lower hardware cost of the PC. used to analyze gels, autoradiographs, Rasband faced a major challenge: how to and computed tomography, magnetic The move to other operating systems continue a program for the Mac and yet resonance and positron emission As the code could be freely used in any support one for the PC. Rasband did not tomography images. form, NIH Image was used in a variety want to port NIH Image to the PC and As a successor to ‘Image’, Rasband of cases, including spinoffs and related did not want to maintain two programs or set out to build a program that would programs such as Scion Image (Scion trust a third party to maintain one. provide the same utility but could be used Corporation) for the personal computer In 1995 Sun Microsystems created on the desktop computers that were just (PC) platform. Scion Image was a notable the Java programming language and becoming widely available, chief among effort by the Scion Corporation to address runtime environment in a bid to create an them the Mac II. With its relative low cost an unmet need—providing an NIH operating system–agnostic programming of adoption, widespread use, easy graphic Image for the PC (Microsoft Windows platform that would allow programmers to interface and good developer support, the operating system) community. In the ‘write once, run anywhere’, freeing them Mac II was the ideal platform for a new early 1990s the PC had caught up to the from having to choose what operating ‘Image’ program. The Mac II had several Mac and had the graphics functionality system to support. Rasband found this key additions over the earlier Mac that and extensibility needed to run a program idea appealing and liked the idea of made Rasband’s vision of NIH Image such as NIH Image, but the NIH Image maintaining a single code base that could possible, specifically (i) expansion slots: program was only available for the Mac. run in any operating system with the the ability to add third-party acquisition Scion Corporation’s products were very Java runtime environment installed or boards, (ii) advanced graphics: the popular with NIH Image users because they on a Web browser as a Java applet, thus ability to handle not only color but most made a frame-grabber board that was the allowing a single program to be run not importantly 8-bit 256 gray colors, the principal way users collected their images only on the Mac and Windows platforms mainstay format of light microscopy, and in NIH Image, whether from a gel imager but also on the Unix operating system that (iii) support for the Pascal programming or analog microscopy camera. Scion saw was becoming popular among scientists. language to allow third-party developers the opportunity to expand its hardware Furthermore, after using Pascal for over 20 to easily develop their own applications. framegrabber market to the PC by making years, Rasband was ready to try another © 2012 Nature America, Inc. All rights reserved. America, Inc. © 2012 Nature In the spring of 1987, just a few months a Windows version of NIH Image.