acqMN.bsh

/**
 * Script used to run another script once for every position during 
 * a Micro-Manager acquisition
 */
import org.micromanager.api.MultiStagePosition;
import org.micromanager.api.MMAcquisition;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.util.prefs.Preferences;
import java.awt.Color;


script = "D:\\projects\\mnfinder\\mn2.bsh";
channelGroup = "Channels";
imagingChannel = "Epi-Cy5-PhotoTarget";
afterZapChannel = "Epi-Cherry";
nrImagesPerWell = 100;
saveLocation = "D:\\Users\\Susana\\20150427\\screen2";
saveZappedLocation = saveLocation + "\\Zapped";


/*
script = "/Users/nico/git/mnfinder/mn2.bsh";
channelGroup = "Channel";
imagingChannel = "DAPI";
afterZapChannel = "FITC";
nrImagesPerWell = 2;
saveLocation = "/Users/nico/tmp/testSreen";
saveZappedLocation = saveLocation + "/Zapped";
*/

//////////DO NOT EDIT BELOW THIS LINE////////////////

// maintain some form of persistence using prefs
prefs = Preferences.userNodeForPackage(this.getClass());
	
gui.closeAllAcquisitions();
new File(saveLocation).mkdirs();
//new File(saveZappedLocation).mkdirs();
resultsFile = new File(saveLocation + File.separator + "results.txt");
resultsFile.createNewFile();
resultsWriter = new BufferedWriter(new FileWriter(resultsFile));

posList = gui.getPositionList();
positions = posList.getPositions();
currentWell = "";
count = 0;
for (int p = 0; p < positions.length; p++) {
	msp = positions[p];
	label = msp.getLabel();
	well = label.split("-")[0];
	if (!currentWell.equals(well)) {
		gui.message ("Starting well: " + well);
		if (!currentWell.equals("")) {
			nuclei = prefs.getInt("nuclei", 0);
			prefs.putInt("nuclei", 0);
			zappedNuclei = prefs.getInt("zappedNuclei", 0);
			prefs.putInt("zappedNuclei", 0);
			resultsWriter.write(currentWell + "\t" + nuclei + "\t" + zappedNuclei);
			resultsWriter.newLine();
			resultsWriter.flush();			
		   gui.message(currentWell + " " + nuclei + "   " + zappedNuclei);
		}
		currentWell = well;
		gui.openAcquisition(well, saveLocation, 1, 2, 1, nrImagesPerWell, true, true);
		wellCount = 0;
	}
	MultiStagePosition.goToPosition(msp, mmc);
	gui.message("Site: " + msp.getLabel());
	mmc.setConfig(channelGroup, imagingChannel);
	mmc.snapImage();
	tImg = mmc.getTaggedImage();
	gui.addImageToAcquisition(well, 0, 0, 0, wellCount, tImg);
	prefs.putInt("zappedNow", 0);
	// run the script recognizing the micronuclei and zapping them
	source(script);
	zappedNow = prefs.getInt("zappedNow", 0);
	if (zappedNow > 0) {
		acq2 = msp.getLabel();
		gui.message("Imaging zapped cells at site: " + acq2);
		// take the red image and save it
		mmc.setConfig(channelGroup, afterZapChannel);
		mmc.snapImage();
		tImg2 = mmc.getTaggedImage();
		gui.addImageToAcquisition(well, 0, 1, 0, wellCount, tImg2);
		acqObject = gui.getAcquisition(well);
		acqObject.setChannelColor(1, new Color(255, 0, 0).getRGB());
		mmc.setConfig(channelGroup, imagingChannel);
	}
	wellCount++;
	count++;
}

// record the results from the last well:
nuclei = prefs.getInt("nuclei", 0);
prefs.putInt("nuclei", 0);
zappedNuclei = prefs.getInt("zappedNuclei", 0);
prefs.putInt("zappedNuclei", 0);
resultsWriter.write(currentWell + "\t" + nuclei + "\t" + zappedNuclei);
resultsWriter.newLine();			
gui.message(currentWell + " " + nuclei + "   " + zappedNuclei);

resultsWriter.close();
gui.message("Analyzed " + count + " images");