If you perform a search for "imagej" on some popular academic databases (such as PubMed (http://www.ncbi.nlm.nih.gov/pubmed), IEEE Xplore (http://ieeexplore.ieee.org/), or Google Scholar (http://scholar.google.com), you will find that this software has been successfully used in a huge number of scientific papers in fields that span several disciplines, from confocal microscopy to X-ray analysis, vehicle license plate detection, ultrasound diagnosis of breast cancer, development of automatic 4D segmentation algorithms or tomographic image reconstruction, to cite just a small sample.
ImageJ is not intended to serve as a replacement for Adobe Photoshop, GIMP, or any other graphics editing program. It is less centered on layers, transparencies, cloning, or blurring, and more on quantification, filtering, measuring, and mathematical processing. This does not mean that an image cannot be modified using ImageJ, but the type of modification that ImageJ is intended to do is of a different nature than that of the programs mentioned previously.