Hi All,

I’m new to ImageJ image processing and have a question about drawing multiple custom ROIs on an image and saving each ROI as a distinct TIFF. I’m working with images of a rodent brain, and I need to divide the brain into 8 different regions that vary in size and shape. *(see image of brain)

I’d love to have a macro that can do the following:

The final products should be the .rois for each polygon boundary that I created and added to my ROI manager and TIFF files for each polygon boundary.*(see image of brain with boundaries denoted)

I have a macro that allows me to crop and save images with custom naming syntax, but I’m struggling to modify it to do everything that I need. Here’s the macro that I’ve been using to achieve cropping and saving ROIs, but again, it’s not quite what I need.

I’d love to hear your thoughts and get feedback! Thanks! (Question cross-posted on image.sc)

//Use this macro for cropping hippocampal sub-regions

regionsToDo = newArray(“_CA1_L”,“_CA1_R”, “_CA2_L.1”,“_CA2_R.1”,“_CA2_L.2”,“_CA2_R.2”, “_CA3_L”,“_CA3_R”, “_DG_L”,“_DG_R”);

// Create anatomical ROIs within each image in a folder dir = getDirectory(“Choose directory to CROP ROIs from slices”); // prompts user to select the folder to be processed, stores the folder as the destination for saving list = getFileList(dir); // gives ImageJ a list of all files in the folder to work through print(list.length); // optional prints the number of files in the folder dir2 = getDirectory(“Choose a Directory for SAVING the ROIs”); // prompts user to select the folder where files will be SAVED

// Function for cropping based on a region. This function is called in the main processing loop. function getRegionCrop(nameNoExtension, dirToSave, regionName) { t2 = nameNoExtension + regionName; //adds regionName to the original name of the image (“t” below). run(“Duplicate…”, “duplicate”); setTool(“line”); waitForUser(“Draw the scale bar”); run(“Set Scale…”, “known=10 unit=cm”); //edit this line to reflect actual size & units of scale bar setTool(“polygon”); waitForUser(‘Please Select the ’ + regionName + ’ ROI’);

//if no selection is possible, need to skip a step if (selectionType() == 3 || selectionType() == 2) {regionSelected = true;} else {regionSelected = false;} //if selection is possible, crop out selection and bound it. if (regionSelected) { run(“Crop”); setBackgroundColor(0, 0, 0); //clear the stuff we don’t want. run(“Clear Outside”); //eliminate data outside of ROI run(“To Bounding Box”); saveAs(“Tiff”, dir2 + t2 + “_” + “Cropped” + “.tif”); } else { closeWindows=getBoolean(“Close window?”); if (closeWindows) { run(“Close”); } } run(“Close”); }

// Close everything before we start. run (“Close All”);

// main files processing loop for (f=0; f=1) { //use the different channels to illuminate cells and landmarks start = getTime(); //optional get start time to see how long a process will take. Goes with last line print time

t=getTitle(); //gets the name of the image being processed s=lastIndexOf(t, '.'); //next three lines are code to strip off the .tif extension from the filename t=substring(t, 0,s); t=replace(t," ","_"); t=replace(t, "hippocampus_ROI", "_");

// Pass the Array of anatomical regions to a cropping Function. Go through each region in the Array, for (thisRegion=0; thisRegion < regionsToDo.length; thisRegion++) { getRegionCrop(t, dir2, regionsToDo[thisRegion]); //getRegionCrop function defined above. getRegionCrop(nameNoExtension, dirToSave, regionName) } run(“Close”); //when done, close the image. } }