Its sources live in a public Git repository.įiji was accepted as organization into the Google Summer of Code 2009, and completed two projects. įiji was prominently featured in Nature Methods review supplement on visualization. The Fiji component TrakEM2 was successfully used and enhanced to analyze neuronal lineages in larval Drosophila brains. įiji is most popular in the life sciences community, where the 3D Viewer helps visualizing data obtained through light microscopy, and for which Fiji provides registration, segmentation, and other advanced image processing algorithms. As stated on the official website, the primary focus is "life sciences", although Fiji provides many tools helping with scientific image analysis in general. While Fiji was originally intended for neuroscientists (and continues to be so ), it accumulated enough functionality to attract scientists from a variety of fields, such as cell biology, parasitology, genetics, life sciences in general, materials science, etc. As a consequence, Fiji enjoys more and more active users. One of Fiji's principal aims is to make the installation of ImageJ, Java, Java 3D, the plugins, and further convenient components, as easy as possible. įurther, some plugins require specific versions of ImageJ, specific versions of third-party libraries, or additional Java components such as the Java compiler or Java 3D. Many plugins exist for ImageJ, that have a wide range of applications, but also a wide range of quality. Fiji features an integrated updating system and aims to provide users with a coherent menu structure, extensive documentation in the form of detailed algorithm descriptions and tutorials, and the ability to avoid the need to install multiple components from different sources.įiji is also targeted at developers, through the use of a version control system, an issue tracker, dedicated development channels, and a rapid-prototyping infrastructure in the form of a script editor which supports BeanShell, Jython, JRuby, Clojure, Groovy, JavaScript, and other scripting languages, as well as just-in-time Java development. Please contact the moderators of this subreddit if you have any questions or concerns.Fiji ( Fiji Is Just ImageJ) is an open source image processing package based on ImageJ2.įiji's main purpose is to provide a distribution of ImageJ2 with many bundled plugins. I am a bot, and this action was performed automatically. If someday your work gets published, show it off here! That's one use of the "Research" post flair. "Time is the most precious gift in our possession, for it is the most irrevocable." ~ DB Remember that "free help" costs those who help:Īside from Automoderator, those responding to you are real people, giving up some of their time to help you. Karma is a small way to say "thanks" and "this was helpful". Upvote those who contribute to the discussion. (See: xkcd 979)Ĭonsider saying "thank you" in comment replies to those who helped. People from the future may be stuck trying to answer the same question. If you figure out the answer for yourself, please post it! Never delete your post, even if it has not received a response.ĭon't switch over to PMs or email. Respond when helpful users ask follow-up questions, even if the answer is "I'm not sure". Image analysis is interdisciplinary, so the more general the terminology, the more people who might be able to help.īe thorough in outlining the question(s) that you are trying to answer.Ĭlearly explain what you are trying to learn, not just the method used, to avoid the XY problem. Good places to upload include:, , & Īvoid discipline-specific terminology ("jargon"). Screenshots (to help identify issues with tools or features) Reference Images (taken from published papers)Īnnotated Mock-ups (showing what features you are trying to measure) Images give everyone a chance to understand the problem.Įxample Images (what you want to analyze) Notes on Quality Questions & Productive Participation
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