The background of the thresholded image can be made light or dark. The Color space option allows you to choose between HSB, RGB, Lab, and YUV. The Threshold color option allows you to choose between Red, White, Black, or B&W as the thresholding color. The Thresholding method option allows you to choose a thresholding techniqe other than the default. Run("Set Scale.For color images, setting the threshold is done with the command sequence Image › Adjust › Color Threshold. PM me if you need a more in depth explanation. basically all this does is measure the area of your entire image in pixels, then it thresholds for your selected colour (see the //commented section, you may need to alter the HSV values a bit), creates a binary selection of that and then measures the area occupied by that colour. Please contact the moderators of this subreddit if you have any questions or concerns.Ĭopy and paste the below into your script editor in imagej and run it as an ijm file and it should work for your open image (file>new>script then select language as IJM1). I am a bot, and this action was performed automatically. Don't make your robotic overlord angry.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.Aside from Automoderator, those responding to you are real people, giving up some of their time to help you.Remember that "free help" costs those who help:.Karma is a small way to say "thanks" and "this was helpful". Upvote those who contribute to the discussion.Consider 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!.Do not delete your post if it has received any response.Respond when helpful users ask follow-up questions, even if the answer is "I'm not sure".Clearly explain what you are trying to learn, not just the method used, to avoid the XY problem.Be thorough in outlining the question(s) that you are trying to answer.Image analysis is interdisciplinary, so the more general the terminology, the more people who might be able to help. Avoid discipline-specific terminology ("jargon").Screenshots (to help identify issues with tools or features).Annotated Mock-ups (showing what features you are trying to measure).Reference Images (taken from published papers).Example Images (what you want to analyze).Images give everyone a chance to understand the problem.Notes on Quality Questions & Productive Participation ¹This subreddit is not affiliated with the creators of ImageJ or FIJI, but is simply a place to share ideas, papers, resources, and expertise - especially as relate to questions & answers posted here. Sign-up for one of the mailing lists: /Mailing_Lists ![]() It also hosts a forum for interacting with the developers.įIJI Is Just ImageJ - "a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure." is full of ImageJ development and analysis resources. Image analysis is interdisciplinary, so clearly explain field-specific terms or jargon. Clearly explain what you are trying to learn, not just the method used, to avoid the XY problem. Provide details: Be thorough in outlining the question(s) that you are trying to answer.People from the future may be stuck trying to answer the same question. Report spam or content that is hateful or off-topic.Upvote those who contribute to the discussion and provide freely of their time to assist you.Projects: Share a Link to your pet image analysis project.Research: Links to published (articles in scientific journals or in established repositories) that utilize ImageJ/FIJI for image analysis or are about image analysis.Discussions: Text posts, meant to ask about general issues relating to image analysis.Image analyst job posts are also welcome. Tips: Text or Link posts to share useful how-to tricks and discoveries on using ImageJ/FIJI.Questions which have been Solved will be marked as such. ![]() This could include algorithms, microscopy and scientific imaging, plug-ins, methods, and specific features of the software. Questions: Text posts asking about image analysis and ImageJ/FIJI.This is a an unofficial¹ forum to discuss image analysis, software features, to get help, to share ideas, and to share work done using ImageJ or FIJI. It's used worldwide, by a broad range of scientists. ![]() ImageJ is a freely available, open source image processing and analysis program using Java, on which FIJI is based.
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