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  • Image Thresholding

Image Thresholding#

We want to apply a threshold to this image. We could just pick a number that works well for this image but remember, we're trying to make a script that we could potentially apply to many images. If we select one number that works with this image, it might not work as well with other images. 🤔

A better approach is to select an autothreshold method. 🚀

Add to your script steps to threshold both images using ImageJ's autothreshold feature. Hint: You might want to make copies of these files before you threshold them, so that we have the raw images to work with later! 
open("path/to/file/bax_DAPI_overlay.tif");
run("Split Channels");
selectWindow("C1-bax_DAPI_overlay.tif");
rename("nuclei");
selectWindow("C2-bax_DAPI_overlay.tif");
rename("bax");
selectWindow("nuclei");
run("Duplicate...", "title=nuclei_thresholded");
run("Auto Threshold", "method=Default white"); //(1)!
selectWindow("bax");
run("Duplicate...", "title=bax_thresholded");
run("Auto Threshold", "method=Default white");
  1. The 'default' method works pretty well here, but feel free to try some other methods and see if you can find a better one!

Oof. our script is getting pretty long, and we haven't even started the analysis. 😱

How could we make our script more easy to read?

Let's use Functions to try to replace some of that duplicated code. 💪