I want to create a macro that will repeat the same process (overlay) several images from two different sets of images. One set is called Fluorescent1...95 (I have 95 images, for example), the other is DIC1...95.
What I need to know is how can I write a macro that tells FIJI (or ImageJ) to overlay Fluorescent1 with DIC1, Fluorescent2 with DIC2, so forth so forth.
Right now, the code is like this:
selectWindow("Fluorescent1");
run("Add Image...", "image=[DIC1.dv] x=0 y=0 opacity=20");
What do I need to change in this code for it to do what I want?
Thank you for your help!
I would suggest you have the files in the same folder. The naming should be consistent for all files - e.g. as you mentioned before. Here is my commented code suggestion - just change it to your needs. Have fun coding! :-)
Best, Martin
-------------------------
// lets you choose your folder
inputDir = getDirectory("Choose your input folder");
// makes a sub directory into your chosen folder
outputDir = inputDir + "results\\";
if(!File.exists(outputDir)) File.makeDirectory(outputDir);
// the highest number you expect (95 in your case)
max = getNumber("How many images do you expect?", 95);
// lets you choose the naming of your files
fluoName = getString("Whats the prefix of your flourescent images?", "Fluorescent");
dicName = getString("Whats the prefix of your DIC images?", "DIC");
// a loop through your images... (1 ... max)
for(i=1; i 0) close();
} else print("At least one file was missing! (" + fluoName + i + " or " + dicName + i + " )");
}
Hi Goncalo,
I sincerely apologize for appearing to hijack this thread and not provide any advice for using Fiji, but I wanted to take the opportunity to recommend you take a our newly released software MIPAR (http://MIPAR.us). It was designed specifically to make tasks like the one you mention extremely efficient and user friendly. Even if you don't use any of other apps or segmentation tools (which I think you would!), in the Processed Image Editor, you can just load in the images you wish to overlay/outline/colorize, and the originals, click through each one, make edits, export them all, make measurements, etc. Best of luck in your research!
Cheers,
John
Hi Gonçalo,
I must apologize - I misread your question. I thought you had multiple segmentation a you needed to overlay. Since you seem to need to overlay multiple color images, with other color images, that is not something could readily handle. However, it may still prove useful in other areas for you. If you have MATLAB, I'd be happy to write a small MATLAB function to perform the overlay task for you. Please let me know.
Cheers,
John
I would suggest you have the files in the same folder. The naming should be consistent for all files - e.g. as you mentioned before. Here is my commented code suggestion - just change it to your needs. Have fun coding! :-)
Best, Martin
-------------------------
// lets you choose your folder
inputDir = getDirectory("Choose your input folder");
// makes a sub directory into your chosen folder
outputDir = inputDir + "results\\";
if(!File.exists(outputDir)) File.makeDirectory(outputDir);
// the highest number you expect (95 in your case)
max = getNumber("How many images do you expect?", 95);
// lets you choose the naming of your files
fluoName = getString("Whats the prefix of your flourescent images?", "Fluorescent");
dicName = getString("Whats the prefix of your DIC images?", "DIC");
// a loop through your images... (1 ... max)
for(i=1; i 0) close();
} else print("At least one file was missing! (" + fluoName + i + " or " + dicName + i + " )");
}
- Badges
- Science topic
- Similar topics
- Engineering
- Electrical Engineering
- Signal Processing
- Image Processing