imagej_open.ijm

// @UIService ui
// @File(label="Raw images directory", description="Images path", style="directory", value="/share/Pariksheet/consultations/rnai-screen-tf/results/z_projection") path
// @String(label="Plate name", choices={"160415_015529-V", "501B102", "502B98", "503B99", "507B99"}) plate
// @String(label="Well", value="C03") well
// @File(label="ROI nucleus images directory", description="Images path", style="directory", value="/share/Pariksheet/consultations/rnai-screen-tf/results/cellprofiler/nuc") path_nuc
// @File(label="ROI centromere images directory", description="Images path", style="directory", value="/share/Pariksheet/consultations/rnai-screen-tf/results/cellprofiler/cen") path_cen
// @File(label="ROI ectopic centromere images directory", description="Images path", style="directory", value="/share/Pariksheet/consultations/rnai-screen-tf/results/cellprofiler/ect") path_ect
// @File(label="ROI overlap images directory", description="Images path", style="directory", value="/share/Pariksheet/consultations/rnai-screen-tf/results/cellprofiler/ect_overlap") path_ect_overlap
// @OUTPUT Dataset image

/*
 * Open multiple TIFF files as hyperstack and overlay ROIs.
 */

// Use batch mode for speed and protecting user settings.
setBatchMode(true);
// Clear all ROIs.
if (roiManager("count") > 0) {
	roiManager("deselect")
	roiManager("delete")
}

/** Open hyperstack of the well */
function imOpen(path, plate, well) {
    run("Image Sequence...",
	" open=" + path +
	" file=" + plate + "_" + well +
	" sort");
    run("Stack to Hyperstack...",
	" order=xyctz" +
	" channels=3" +
	" slices=1" +
	" frames=" + nSlices / 3 +
	" display=Composite")
    Stack.setChannel(1);
    run("Blue");
    Stack.setChannel(2);
    run("Red");
    Stack.setChannel(3);
    run("Green");
}
//imOpen(path, plate, well);

/** Import ROIs generated by CellProfiler */
function roiOpen(path, plate, well, color) {
    run("Image Sequence...",
	" open=" + path +
	" file=" + plate + "_" + well +
	" sort");
    getMinAndMax(im_min, im_max);
    im_list = getList("image.titles");
    orig = im_list[lengthOf(im_list) - 1];
    roi_min = roiManager("count");
	// Iterate through all the images to add the ROIs to the ROI manager.
	for (i = 1; i < 3; i++) {//im_max; i++) {
		selectWindow(orig);
	run("Duplicate...", "duplicate");
		setThreshold(i, i);
		run("Convert to Mask", "method=Default background=Dark");
		run("Analyze Particles...", "add stack");
		close();
	}
	roi_max = roiManager("count") - 1;
	// If any new ROIs were added, set an appropriate color.
	if (roi_max + 1 > roi_min) {
	roi_ids = newArray();
	for (i = roi_min; i <= roi_max; i++)
		roi_ids = Array.concat(roi_ids, i);
		roiManager("select", roi_ids);
		roiManager("Set Color", color);
	}
}

roiOpen(path_nuc, plate, well, "blue");
roiOpen(path_cen, plate, well, "green");
roiOpen(path_ect, plate, well, "red");

// Only show ROIS in current slice.
roiManager("Associate", "true");
roiManager("Show All");

setBatchMode(false);