Please contact the moderators of this subreddit if you have any questions or concerns. 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 I would also like to expand this to three channels at some point so any help there would be epic too! Where am I going wrong? If I have missed any useful or relevant information please let me know and I will add it. Run("Merge Channels.", "c1=" + channel2 + " c3=" + channel1 + " create") The images save but they are very blurry and the colours are very bright, I am unsure of the technical term, but the image is not as crisp or clear (image below, left)Ĭhannel1 = "C1-" + File.name // = "C1-confocal-series-1.tif" The issue comes when I try to use this in the batch process function in ImageJ. Run("Merge Channels.", "c1=" + channel1 + " c2=" + channel2 + " create") Īnd it gets me the image I want (image below, right) I created this macro: channel1 = "C1-" + File.name // = "C1-confocal-series-1.tif"Ĭhannel2 = "C2-" + File.name // = "C2-confocal-series-1.tif" When I do the image analysis steps manually this is the protocol I follow:Ĭ1 (red) C1-XXX, C2 (green) none, C3 (blue) C2-XXX (-XXX just denotes the channel nameim selecting).Īnd I get the image I want (it is clear), then I save it as a Tiff. I'm new to ImageJ and trying to figure out macros and batch processing.
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