Confocal and TIRF on Scope 7

confocal-plus-TIRF.bsh

// Test acquisition script
// Modified from http://www.micro-manager.org/w/images/3/33/TestAcq.bsh (Nenad Amodaj, feb2008)

import org.micromanager.api.AcquisitionOptions;

// clear all previous acquisitions
gui.closeAllAcquisitions();
gui.clearMessageWindow();

// file locations

rootDirName = "E:/Hiro/20131126/01 FC1";

// parameters
numFrames = 10;
intervalMs = 0;

/*
acqName_confocal = "acq_confocal";
channelGroup_confocal = "confocal-EMCCD";
String[] channels_confocal = {"488confocalEM", "561confocalEM"};
Color[] colors = {Color.GREEN, Color.RED};
int[] exposures_confocal = {100, 100};
numSlices = 10;

acqName_tirf = "acq_tirf";
channelGroup_tirf = "TIRF-Flash4";
String[] channels_tirf = {"488tirf", "561tirf"};
Color[] colors = {Color.GREEN, Color.RED};
int[] exposures_tirf = {30, 30};
*/

acqName = "tirf-confocal";

channelGroup_confocal = "Channel";
String[] channels_confocal = {"FITC", "Rhodamine"};
Color[] colors = {Color.GREEN, Color.RED};
int[] exposures_confocal = {100, 100};
numSlices = 10;

// acqName_tirf = "test-acq-col2";
channelGroup_tirf = "Channel";
String[] channels_tirf = {"FITC", "Rhodamine"};
Color[] colors = {Color.GREEN, Color.RED};
int[] exposures_tirf = {30, 30};




float[] zpositions = new float[numSlices];
for(int i=0;i<numSlices;i++){
	zpositions[i] = new Float(0.5*new Float(i) + 1.0);
}

// create acquisition and set options
gui.openAcquisition(acqName, rootDirName, numFrames, channels.length, numSlices+1);

for (int i=0; i<colors.length; i++)
   gui.setChannelColor(acqName, i, colors[i]);

for (int i=0; i<channels.length; i++)
   gui.setChannelName(acqName, i, channels[i]);

zdefault = 0;

for(int k=0;k<numFrames;k++){

   mmc.fullFocus();

   for (int j=0; j<channels_tirf.length; j++) {
      gui.message("Acquiring frame " + i + ", channel " + channels[j] + ".");
      mmc.setExposure(exposures_tirf[j]);
      mmc.setConfig(channelGroup_tirf, channels_tirf[j]);
      mmc.waitForConfig(channelGroup_tirf, channels_tirf[j]);
      gui.snapAndAddImage(acqName, k, j, 0);
   }

   // set channel contrast based on the first frame
   if (i==0) {
      gui.setContrastBasedOnFrame(acqName, i, 0);
   }

      mmc.setExposure(exposures_confocal[0]);
      mmc.setConfig(channelGroup_confocal, channels_confocal[0]);
      mmc.waitForConfig(channelGroup_confocal, channels_confocal[0]);

for (int i=0; i<numSlices; i++) {
	z = zpositions[i];
	//safe within 20 um
	if(z >= -20 && z <= 20){
		mmc.setRelativePosition(mmc.getFocusDevice(), z);
		mmc.setProperty("Z","Position",""+z);
	}
   
   for (int j=0; j<channels_confocal.length; j++) {
      gui.message("Acquiring frame " + i + ", channel " + channels[j] + ".");
      mmc.setExposure(exposures_confocal[j]);
      mmc.setConfig(channelGroup_confocal, channels_confocal[j]);
      mmc.waitForConfig(channelGroup_confocal, channels_confocal[j]);
      gui.snapAndAddImage(acqName, k, j, i+1);
   }

   // set channel contrast based on the first frame
   if (i==0) {
      gui.setContrastBasedOnFrame(acqName, i, 0);
   }
}
   gui.sleep(intervalMs);
}

mmc.setRelativePosition(mmc.getFocusDevice(),zdefault);