ENH: Read image and ROI stacks in ImageJ

src/imagej_open.ijm

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+// @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);