![]() For most newer laptops, 64-bit is the correct choice. They can find this by accessing the Control Panel, System Properties (System and Security), System, System type. PC users need to choose the correct version to match their version of Java. Students will need to choose the correct version to match their laptop. This software will be used for over half of the labs and for occasional homeworks, so it is good for students to have access on their laptop/home computer. ImageJ software is used in lots of biomedical research labs-some students may already be familiar with it/have heard of it. Students will learn more about this in the pre-reading to a future lab (Lab 1b). One of the modern tools that we will use is an image/video analysis software called ImageJ. How to Download ImageJ (w/ "Manual Tracking" and "MultiTracker" plug-ins.) The old multitracker is not included if you want to use it you can get it from and put it in your plugins folder.A new multitracker called MTrack2 is also included in the plugins menu and is much better than the old one.Manual Tracking is located in plugins->tracking.Run the “ImageJ” application that’s inside the Fiji.app folder. To Install, extract all the files from the.(In theory, there is also an object segmentation workflow which I haven't tried yet, I stuck to the simplest pixel classification our of convenience).Fiji is ImageJ, but with many plugins already included. You can then let Ilastik train its segmenter on your input and get a probability map that you can process further in Fiji. You can set a portion of your data aside for training (a couple images should suffice), and annotate a couple fishes. trainable WEKA Segmenter), but I personally find Ilastik as a standalone program to be easier to work with. If all else fails you can jump right ahead to machine-learning for object recognition. ![]() With a bit of luck it will pick up the brightness gradient of the riverbed and remove it. ![]() You could try more advanced background reduction such as the built-in pseudo-flat-field correction ( see here, section 7.1.2). However it might end up emphasizing other bright structures. This should help clean up small irregularitires. Try the built-in background reduction (Filters -> Subtract background) with a large radius, e.g. (I'm assuming that you want to count the dark long things and exclude everything else). Hm, sounds like a background reduction task. 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
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