like - circularity 0 - 2 etc… I can help u with this later. with the analyze particles, once you know what you want as presettings, Below is a way to shorten the time effing you can comment out this “close until you are sure the program runs well… ImageCalculator(“AND create 16-bit”, img5, img6) rename("AND of CFOS and CHAT") OR YOU CAN switch to using the run analyze particles… ImageCalculator(“AND create 16-bit”, img3, img4) you can comment out this close if you want to see the “AND” image Run(“Analyze Particles…”, “size=0.00-Infinity circularity=0.00-5.00 include summarize”) Particle counting can be done automatically if the specimen lends itself to it, i.e. Select the type you want to count, and count by clicking on the feature in the image. Note that at any time you can add types or remove them. Click initialize, now you are ready to count features. ImageCalculator(“AND create 16-bit”, img1, img2) Open the Cell Counter plugin and the image/stack you want to count (if the Cell Counter plugin is already open you don't need to open a new instance). Below are possible threshold you can use for the diff WaitForUser(“choose next window for threshold Chat”) WaitForUser(“choose next window for threshold CFOS”) Run(“Analyze Particles…”, “size=0-Infinity circularity=0.00-5.00 clear include summarize”) WaitForUser("choose threshold for red than click ok. WaitForUser(“choose next window for threshold DAPI”) ShowMessage("select image for analysis ") If you’re interested, we have some example pipelines, including a colocalization example, on the website.įor anyone using IMAGE J / FIJI. Using the Analyze Particles function in ImageJ to count fluorescent particles DIY Biosensors 43 subscribers Subscribe 29 Share 1.8K views 11 months ago Quick tutorial for how to threshold your. There are also options for this type of analysis in CellProfiler, which might be a good option particularly if you are new to macro writing (in CellProfiler, you select customizable analysis modules but there isn’t the same coding required in writing ImageJ macros). If you do these steps manually with the Macro Recorder on, it will record the macro commands used to trigger those actions so you can paste them into a macro (File > New > Text Window).
0 Comments
Leave a Reply. |