If you then get completely stuck somewhere or don’t understand a specific topic, feel free to ask on those specifically. So, first set out to read in the resources and try some on your own. With all due respect you cannot expect that those who offer help here do all the work for you. This forum is definitely here to help you with this journey but this means you will also need to show some effort and willingness to read on how to use ImageJ and the macro language and test things on your own. Having a specific goal and image material to try, is the best starting point in getting more proficient in the area of image analysis. There is a lot more material to learn from but you need to start somewhere. Learning the macro language is relatively easy even if you did never program before.īut that is just half of the game, since some understanding of image processing is also necessary to know which steps make sense to put in such a sequence dependent on the image material as well as the objective of the analysis.Ī few principles are explained here, here and here. ![]() There are a few resources to get into the ImageJ Macro Language and specific commands commands. Run("Analyze Particles.", "size=5000-Infinity display exclude clear stack") Run("EDM Binary Operations", "iterations=40 operation=open stack") ![]() Run("Auto Threshold", "method=Li stack") Run("Pseudo flat field correction", "blurring=50 hide stack") It has developer API that can be used to implement new plugins for specific image processing tasks. Macro: run("Set Measurements.", "area perimeter fit feret's display redirect=None decimal=3") ImageJ is an open-source application widely used for image processing. how variable the size of the objects will be.If you can still work on the lighting of the scene and the contrast of the imaging setup, that will surely positively influence the analysis. There is already a slight lighting problem in your example movie. how standardized your lighting and imaging will be.How well that works on your other images depend on This might influence the result to some extend. Since the droplet is quite connected with the other longer structure in the image, it was not possible to separate those two perfectly. My suggestion would be to check if either the value Minor or MinFeret (explained here) gives you your desired readout. In the end you will receive a table with different columns. Give it a little time since it needs to process over 500 slices but you will see that something happens. press the Run button in the lower left corner in the script editor.open your movie file in Fiji by drag ‘n’ drop.Press + to open the Fiji script editor.install the BioVoxxel update site in Fiji.download Fiji (if you are currently using plain ImageJ).To make the macro work, please follow these steps: Hi can try the macro below and see if that gives you the desired values.
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