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I am working on a project in which I am attempting to analyze a fish within a petri dish using ImageJ and an AVI clip of the fish under a microscope. My first hurdle is to locate the fish within the dish, which I assume I could do without even needing the entire stack (maybe even just a single frame). I am new to image processing, but with the libraries available in ImageJ, I am hoping to be able to locate the edge of the fish and either cut out that edge or cut out a smaller box containing just the fish. Any help would be greatly appreciated from those of you with experience in either ImageJ or image processing in general. Thanks!

Fish within the petri dish

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  • $\begingroup$ I think your question could be clearer. Do you need help figuring out what steps to take to isolate the fish, or are you asking how to write code for imageJ to do that task or both? $\endgroup$ – JRE Sep 9 '15 at 13:20
  • $\begingroup$ How consistent is the lighting? $\endgroup$ – geometrikal Sep 9 '15 at 14:08
  • $\begingroup$ @JRE - Sorry for the lack in clarity. My goal overall would be to write this as a plugin in ImageJ - I have everything setup to run code via a plugin. I would assume that by learning how to do it manually, I could attempt to write the code to run in place. I am a strong programmer, but I do lack the knowledge in image processing techniques - use of filters, etc. $\endgroup$ – Michael Sep 9 '15 at 14:14
  • $\begingroup$ @geometrikal - The lighting is pretty consistent and the fish primarily lies on the outer edge of the petri dish. I am trying to avoid any techniques that are too specific to this microscope, in hopes to get the same algorithm to work in the case that a different microscope is used. $\endgroup$ – Michael Sep 9 '15 at 14:15
  • $\begingroup$ OK, so you are looking for the manual steps to isolate the fish (manually drawing a selection box NOT allowed,) which you will then automate in ImageJ? $\endgroup$ – JRE Sep 9 '15 at 14:16

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