Hey ImageJ gurus,
there are some discussions ongoing in parallel about our ImageJ2/Fiji documentation. I’m just searching for a good written online tutorial on how to switch from ImageJ macro to an advanced mode. Assume, I come from a non-computer-science field. Maybe I don’t know anything about objects, classes, java, python, jython, groovy, git, maven. But I’m an advanced macro coder for years. Do we have documentation for this audience?
I’m in particular wondering how to translate my favorite workflow: CCA on blobs.gif
This is how it looks in macro:
// load image run("Blobs (25K)"); // correct LUT run("Invert LUT"); // preprocessing: filtering run("Gaussian Blur...", "sigma=2"); // thresholding setAutoThreshold("Default dark"); setOption("BlackBackground", true); run("Convert to Mask"); // configure measurements run("Set Measurements...", "area redirect=None decimal=3"); // connected components analysis run("Analyze Particles...", " show=[Count Masks] display"); // result visualisation run("glasbey on dark");
I know that this workflow can be quite complicated in ImageJ2, but it contains basically everthing you need to understand to switch to ImageJ2: Imgs, Ops, Regions, Labels, Tables. Is there a written online tutorial out there how to do such a translation? Either for the script editor (Jython/Groovy) or using IDEs (Java).
Any link is welcome!