MicroManager_AutoScanJ_Tiling.bsh

import java.net.ServerSocket;
import java.net.UnknownHostException;
import java.io.IOException;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.OutputStream;
import java.util.*;
import org.micromanager.api.AcquisitionOptions;
import org.micromanager.navigation.*;
import java.util.Date;
import java.text.SimpleDateFormat;
import ij.process.*;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.*;

/*************************************************************************************************/

/** Camera */
XChip = 1344;
YChip = 1024;

/** Secondary scan ROI (binning 1 coordinates system) */
XRoi = 336;
YRoi = 256;
RoiWidth = 672;
RoiHeight = 512;

/** AF */
AFEnabled = true;
AFMode = "Auto";  /** "Manual" or "Auto" */
AFFirstManual = true;
/** Tested with: OughtaFocus 50/1/1/15/No/StdDev + Binning 4 */

/** Channels */
ChannelAF = "DAPI";
String[] channelslow = {"DAPI"};
String[] channelshigh = {"DAPI","FITC","Cy5"}; 

/** Dialog box */
gd = new ij.gui.GenericDialog("AutoScanJ");
gd.addStringField("Scan folder: ", "E:/MMCAM");
gd.addNumericField("NRow: ", 2, 0);
gd.addNumericField("NCol: ", 2, 0);
gd.addNumericField("Low pix size: ", 0.3225, 4);
gd.addNumericField("NStep low: ", 1, 0);
gd.addNumericField("ZStep low: ", 5, 2);
gd.addNumericField("NStep high: ", 5, 0);
gd.addNumericField("ZStep high: ", 0.25, 2);
gd.showDialog();
ScanFolder = gd.getNextString();
NRow = (int)gd.getNextNumber();
NCol = (int)gd.getNextNumber();
LowPixSize = (float)gd.getNextNumber(); /** microns */
nzStepslow = (int)gd.getNextNumber();		
zSteplow = (float)gd.getNextNumber(); /** microns */
nzStepshigh = (int)gd.getNextNumber();		
zStephigh = (float)gd.getNextNumber(); /** microns */
if (gd.wasCanceled())return; 

/** Advanced parameters */

/** Stage configuration */
FlipXY = 0;
XSign = 1;
YSign = 1;

/** Image file prefix */
ImageName = "image";

/** PRIMARY SCAN */
/** Grid spacing (only used for AutoGrid = 0) */
XStep = 500; /** microns */
YStep = 500; /** microns */
AutoGrid = 1; /** Overwrite XStep and YStep by using pixel size information */

/** SECONDARY SCAN */
/** User defined XYZ Offsets */
xOffHigh = 0; /** microns */
yOffHigh = 0; /** microns */
zOffHigh = 0; /** microns */
/** AF offset */
zOffAF = 0; /** microns */

/*************************************************************************************************/

/** Initialization */
gui.closeAllAcquisitions();
gui.clearMessageWindow();
boolean ExitScan = false;
boolean AFCommand = false;
int ScanMode = 0;

/** Set primary scan configuration */
mmc.setConfig("Camera", "PrimaryScan");
mmc.waitForConfig("Camera", "PrimaryScan");
mmc.setConfig("Channel", channelslow[0]);
mmc.waitForConfig("Channel", channelslow[0]);

/** Get devices */
xystage = mmc.getXYStageDevice();
zstage = mmc.getFocusDevice();

if(FlipXY == 1)
{
	buf = XSign;
	XSign = YSign;
	YSign = XSign;
}

/** Empty string */
String Astring = "";

/** Stage XY reference */
gd = new ij.gui.GenericDialog("Reference position"); 
gd.addMessage("Set stage reference position numerically?");
gd.showDialog();
if(!(gd.wasCanceled()))
{ 
	xRef = mmc.getXPosition(xystage);
	yRef = mmc.getYPosition(xystage);
	gd = new ij.gui.GenericDialog("Stage reference position");
	gd.addNumericField("X reference position (microns): ", xRef, 2);
	gd.addNumericField("Y reference position (microns): ", yRef, 2);
	gd.showDialog();
	xRef = gd.getNextNumber();
	yRef = gd.getNextNumber();
	/** Round absolute stage position to closest 10 nm multiple */
	mmc.setXYPosition(xystage,(float)Math.round(xRef*100)/100,(float)Math.round(yRef*100)/100);
	mmc.waitForDevice(xystage);
}
else
{
	gui.enableLiveMode(true);
	JOptionPane.showMessageDialog(null, "Position the stage at upper left corner");
	gui.enableLiveMode(false);
	xRef = mmc.getXPosition(xystage);
	yRef = mmc.getYPosition(xystage);
	/** Round absolute stage position to closest 10 nm multiple */
	mmc.setXYPosition(xystage,(float)Math.round(xRef*100)/100,(float)Math.round(yRef*100)/100);
	mmc.waitForDevice(xystage);
}
xRef = mmc.getXPosition(xystage);
yRef = mmc.getYPosition(xystage);
gui.message("xRef: "+xRef+"  yRef: "+yRef);

/** AutoGrid */
if(AutoGrid == 1)
{
	ImgWidth = mmc.getImageWidth();
	ImgHeight = mmc.getImageHeight();
	XStep = LowPixSize*ImgWidth;
	YStep = LowPixSize*ImgHeight;
}

/** Reset ROI */
Binning = Integer.parseInt(mmc.getProperty(mmc.getCameraDevice(), "Binning"));
mmc.setROI(0,0,XChip/Binning,YChip/Binning);

/** Focus map */
zOff = new float [NCol][NRow];
testFile = new File(ScanFolder+"/FocusMap.txt").isFile();
if(testFile)
{
	gd = new ij.gui.GenericDialog("Focus Map"); 
	gd.addMessage("Focus map already acquired, re-acquire?");
	gd.showDialog();
	if(!(gd.wasCanceled()))testFile = false; 
}
if(!testFile)
{
	gui.enableLiveMode(true);
	JOptionPane.showMessageDialog(null, "Upper left corner\nPlease adjust the focus, then press OK");
	gui.enableLiveMode(false);
	zOff[0][0] = (float)mmc.getPosition(zstage);
	if(NCol>1)
	{
		mmc.setXYPosition(xystage,xRef+(NCol-1)*XStep,yRef);
		mmc.waitForDevice(xystage);
		gui.enableLiveMode(true);
		JOptionPane.showMessageDialog(null, "Upper right corner\nPlease adjust the focus, then press OK");
		gui.enableLiveMode(false);
		zOff[(NCol-1)][0] = (float)mmc.getPosition(zstage);
	}
	if(NRow>1)
	{
		mmc.setXYPosition(xystage,xRef,yRef+(NRow-1)*YStep);
		mmc.waitForDevice(xystage);
		gui.enableLiveMode(true);
		JOptionPane.showMessageDialog(null, "Lower left corner\nPlease adjust the focus, then press OK");
		gui.enableLiveMode(false);
		zOff[0][(NRow-1)] = (float)mmc.getPosition(zstage);
	}
	if((NCol>1)&&(NRow>1))
	{
		mmc.setXYPosition(xystage,xRef+(NCol-1)*XStep,yRef+(NRow-1)*YStep);
		mmc.waitForDevice(xystage);
		gui.enableLiveMode(true);
		JOptionPane.showMessageDialog(null, "Lower Right corner\nPlease adjust the focus, then press OK");
		gui.enableLiveMode(false);
		zOff[(NCol-1)][(NRow-1)] = (float)mmc.getPosition(zstage);
	}
	FileWriter fstream = new FileWriter(ScanFolder+"/FocusMap.txt");
	BufferedWriter out = new BufferedWriter(fstream);
	out.write(Float.toString(zOff[0][0])+"\n");
	out.write(Float.toString(zOff[(NCol-1)][0])+"\n");
	out.write(Float.toString(zOff[0][(NRow-1)])+"\n");
	out.write(Float.toString(zOff[(NCol-1)][(NRow-1)])+"\n");
	out.close();
}
else
{
	FileReader fr = new FileReader(ScanFolder+"/FocusMap.txt");
	BufferedReader br = new BufferedReader(fr);
	zOff[0][0] = Float.valueOf(br.readLine());
	zOff[(NCol-1)][0] = Float.valueOf(br.readLine());
	zOff[0][(NRow-1)] = Float.valueOf(br.readLine());
	zOff[(NCol-1)][(NRow-1)] = Float.valueOf(br.readLine());
	fr.close();
}

/** Compute and display z map */
gui.message("Z map:");
for(y=1;y<=NRow;y++)
{
	Str = "";
	for(x=1;x<=NCol;x++)
	{	
		zOff[x-1][y-1] = (zOff[0][0]/((x-1+(float)1e-9)*(y-1+(float)1e-9))+zOff[0][(NRow-1)]/((x-1+(float)1e-9)*(NRow-y+(float)1e-9))+zOff[(NCol-1)][0]/((NCol-x+(float)1e-9)*(y-1+(float)1e-9))+zOff[(NCol-1)][(NRow-1)]/((NCol-x+(float)1e-9)*(NRow-y+(float)1e-9)))/(1/((x-1+(float)1e-9)*(y-1+(float)1e-9))+1/((x-1+(float)1e-9)*(NRow-y+(float)1e-9))+1/((NCol-x+(float)1e-9)*(y-1+(float)1e-9))+1/((NCol-x+(float)1e-9)*(NRow-y+(float)1e-9))); 
		zOff[x-1][y-1] = (float)Math.round(zOff[x-1][y-1]*100)/100;
		Str = Str + zOff[x-1][y-1] + " ";
	}
	gui.message(Str);
}

/** Initialize server socket */
gd = new ij.gui.GenericDialog("Server"); 
gd.addMessage("Initialize server?");
gd.showDialog();
if (gd.wasCanceled())return; 
gui.message("Initiating server on port 8895...");
try 
{
	socketServer = new ServerSocket(8895);
} 
catch (IOException e) 
{
    System.out.println("Could not start server on port 8895");
    return;
}

/** Main loop: wait for primary/secondary scan */
int t = 0;
while(ExitScan == false)
{
gui.message("Waiting for incoming connection...");

/** Wait for incoming connection */
try 
{
	clientSocket = socketServer.accept();
} 
catch (IOException e) 
{
    System.out.println("Could not establish connection with client");
    return;
}

/** Open socket streams */
gui.message("Connection accepted (5s time out)...");
clientSocket.setSoTimeout(5000);
in = new BufferedReader(new InputStreamReader(clientSocket.getInputStream()));
PrintWriter out = new PrintWriter(clientSocket.getOutputStream(), true);

/** Send welcome message to client */
out.println("welcome");

/** Store incoming CAM commands */
String fromClient = null;
boolean test = false;

String [] CommandList = new String[4096]; /** 4096 CAM commands limit!! */
int cntcommands = 0;

while(test == false)
{
	try{
		fromClient = in.readLine();
	}
	catch (IOException e)
	{
		gui.message("Connection timed out, closing socket and exiting...");
		in.close();
		clientSocket.close();
		socketServer.close();
		Thread.stop();
	}
	CommandList[cntcommands] = fromClient;
	cntcommands++;
	test = (fromClient.indexOf("end") > -1);
	if(fromClient.indexOf("startscan") > -1)
	{
		ScanMode = 1;
	}
	if(fromClient.indexOf("startcamscan") > -1)
	{
		ScanMode = 2;
	}
	if(fromClient.indexOf("/ext:af") > -1)
	{
		AFCommand = true;
	}
	if(fromClient.indexOf("exit") > -1)
	{
		ExitScan = true;
	}
}

if(ScanMode == 2)
{
gui.message("CAM SCAN");

/** Generate TimeStamp */
Date dateNow = new Date ();
SimpleDateFormat formateddate = new SimpleDateFormat("yyyy_MM_dd_HH_mm_ss");
StringBuilder datestring = new StringBuilder( formateddate.format(dateNow) );
	
/** Create scan folder */
ScanSubFolder = "scan--"+datestring.toString();	
(new File(ScanFolder+"/"+ScanSubFolder)).mkdir();
CAMScanSubFolder = "CAM1--"+datestring.toString();
(new File(ScanFolder+"/"+ScanSubFolder+"/"+CAMScanSubFolder)).mkdir();

/** SECONDARY SCAN */
/** Set secondary scan configuration */
mmc.setConfig("Camera", "SecondaryScan");
mmc.waitForConfig("Camera", "SecondaryScan");
mmc.setConfig("Channel", channelshigh[0]);
mmc.waitForConfig("Channel", channelshigh[0]);
/** Set secondary scan ROI */
Binning = Integer.parseInt(mmc.getProperty(mmc.getCameraDevice(), "Binning"));
mmc.setROI(XRoi/Binning,YRoi/Binning,RoiWidth/Binning,RoiHeight/Binning);

/** CAM command loop */

/** T filename field */
TIndex = Astring.format("%1$04d",new Object[]{t});
NumHitPerWell = new int[NCol][NRow];
PosCount = 0;
for(int i=0;i<cntcommands;i++)
{
	Buffer = CommandList[i];
	if(Buffer.indexOf("add")>0) 
	{
		PosCount = PosCount+1;
		gui.message("Position index: "+PosCount);
		ind = Buffer.indexOf("wellx");
		ind2 = Buffer.indexOf(" ",ind);
		Strwellx = Buffer.substring(ind+6,ind2); 
		wellx = Integer.parseInt( Strwellx );
		ind = Buffer.indexOf("welly");
		ind2 = Buffer.indexOf(" ",ind);
		Strwelly = Buffer.substring(ind+6,ind2); 
		welly = Integer.parseInt( Strwelly );
		ind = Buffer.indexOf("dxpos");
		ind2 = Buffer.indexOf(" ",ind);
		Strdxpos = Buffer.substring(ind+6,ind2); 
		dxpos = Integer.parseInt( Strdxpos );
		ind = Buffer.indexOf("dypos");
		Strdypos = Buffer.substring(ind+6,Buffer.length()); 
		dypos = Integer.parseInt( Strdypos );
	
		/** Acquire position */
		/** Channel loop */
		for (int c=0; c<channelshigh.length; c++) 
		{
			CIndex = Astring.format("%1$02d",new Object[]{c});
			mmc.setConfig("Channel", channelshigh[c]);
			mmc.waitForConfig("Channel", channelshigh[c]);		

			/** Compute new stage position */
			xOffset = ((wellx-1) * XStep + dxpos*LowPixSize)*XSign;
			yOffset = ((welly-1) * YStep + dypos*LowPixSize)*YSign;
			if(FlipXY == 1)
			{
				buf = xOffset;
				xOffset = yOffset;
				yOffset = buf;
			}
			sx = xOffHigh + xRef + xOffset;
			sy = yOffHigh + yRef + yOffset;
			
			/** Move stage */
			mmc.setXYPosition(xystage,sx,sy);
			mmc.waitForDevice(xystage);
			
			if((AFEnabled == true)&&(AFCommand == true)&&(c == 0))
			{
				/** Compute z drive central position from focus map */
				sz = zOffHigh + zOff[(wellx-1)][(welly-1)];
				
				/** Move z drive */
				mmc.setPosition(zstage,sz);
				mmc.waitForDevice(zstage);

				if(AFMode.equals("Manual")||(AFFirstManual == true))
				{
				/** Live mode for adjustment */
				gui.enableLiveMode(true);
				gd = new ij.gui.GenericDialog("Fine Focus"); 
				gd.addMessage("Adjust the view, leave AF enabled?");
				gd.showDialog();
				gui.enableLiveMode(false);

				if(gd.wasCanceled())AFEnabled = false;
				
				/** Update offsets */
				xOffHigh = xOffHigh+mmc.getXPosition(xystage)-sx;
				yOffHigh = yOffHigh+mmc.getYPosition(xystage)-sy;
				zOffHigh = zOffHigh+mmc.getPosition(zstage)-sz;

				AFFirstManual = false;
				}
				else
				{
				gui.message("Autofocus...");
				mmc.setConfig("Camera", "AFScan");
				mmc.waitForConfig("Camera", "AFScan");
				mmc.setConfig("Channel", ChannelAF);
				mmc.waitForConfig("Channel", ChannelAF);
				
				autofocus = gui.getAutofocus();
				autofocus.fullFocus();
				zOffAF = mmc.getPosition(zstage)-sz;
				gui.message("Autofocus z offset: "+zOffAF);
				
				mmc.setConfig("Camera", "SecondaryScan");
				mmc.waitForConfig("Camera", "SecondaryScan");
				mmc.setConfig("Channel", channelshigh[c]);
				mmc.waitForConfig("Channel", channelshigh[c]);
				/** Set secondary scan ROI */
				Binning = Integer.parseInt(mmc.getProperty(mmc.getCameraDevice(), "Binning"));
				mmc.setROI(XRoi/Binning,YRoi/Binning,RoiWidth/Binning,RoiHeight/Binning);
				}
			}

			/** z loop */		
			for (int z=0; z < nzStepshigh; z++) 
			{
					/** Z filename field */
					ZSliceIndex = Astring.format("%1$02d",new Object[]{z});
				
					/** Compute new z drive position */
					sz = zOffAF + zOffHigh + zOff[(wellx-1)][(welly-1)] + (z-Math.floor(nzStepshigh/2)) * zStephigh;

					/** Move z drive */
					mmc.setPosition(zstage,sz);
					mmc.waitForDevice(zstage);
					      			
					/** Check current stage position and display it */
					xPosc = mmc.getXPosition(xystage);
					yPosc = mmc.getYPosition(xystage);
					zPosc = mmc.getPosition(zstage);
								
					if((z==0)&&(c==0))gui.message("Acquiring stack at frame " + t + " xPos " + xPosc + " yPos "+ yPosc+ " zPos " + zPosc);

					/** Capture image */
					mmc.snapImage();

					/** Copy captured image to ImagePlus structure */
					img = mmc.getImage();
					width = mmc.getImageWidth();
					height = mmc.getImageHeight();
					byteDepth = mmc.getBytesPerPixel();
					if (byteDepth == 1) 
					{
  					 ip = new ByteProcessor((int)width, (int)height);
  					 ip.setPixels(img);
					} 
					else if (byteDepth==2) 
					{
  					    ip = new ShortProcessor((int)width, (int)height);
   				 	 ip.setPixels(img);
					} 
					else 
					{
   					console.message("Unknown byte depth.");
					}
					
					XIndex = Astring.format("%1$02d",new Object[]{wellx-1});
					YIndex = Astring.format("%1$02d",new Object[]{welly-1});
					if(NumHitPerWell[wellx-1][welly-1]==0)
					{
						FilePath = ScanFolder+"/"+ScanSubFolder+"/"+CAMScanSubFolder+"/"+ImageName+"--L0000--S00--U"+XIndex+"--V"+YIndex+"--J00--E00--O00--X00--Y00--T"+TIndex+"--Z"+ZSliceIndex+"--C"+CIndex+".ome.tif";
					}
					else 
					{
						SuppPos = Astring.format("%1$03d",new Object[]{NumHitPerWell[wellx-1][welly-1]});
						FilePath = ScanFolder+"/"+ScanSubFolder+"/"+CAMScanSubFolder+"/"+ImageName+"--L0000--S00--U"+XIndex+"--V"+YIndex+"--J00--E00--O00--X00--Y00--T"+TIndex+"--Z"+ZSliceIndex+"--C"+CIndex+"--"+SuppPos+".ome.tif";
					}
					ImagePlus imp = new ImagePlus(FilePath, ip);					

					/** Show the central z slice, first channel of the first 5 stacks acquired */
					if((z==(Math.floor(nzStepshigh/2)))&&(c==0)&&(i<5))
					{
						ImagePlus buf = new ImagePlus(FilePath, ip);						
						buf.show();
					}
					
					/** Save image to file */
					FileSaver fs = new FileSaver(imp);
					fs.saveAsTiff(FilePath);
			}
		}
		NumHitPerWell[wellx-1][welly-1] = NumHitPerWell[wellx-1][welly-1]+1;
	}
	if(IJ.altKeyDown())
	{
		i = cntcommands;
		gui.message("Secondary scan aborted!");
	}
}

/** End of scan message */
out.println("XY scanfinished");

}

/** PRIMARY SCAN */
if(ScanMode == 1)
{
	gui.message("PRIMARY SCAN");
	/** Current time */
	now = System.currentTimeMillis();

	/** Generate TimeStamp */
	Date dateNow = new Date ();
	SimpleDateFormat formateddate = new SimpleDateFormat("yyyy_MM_dd_HH_mm_ss");
	StringBuilder datestring = new StringBuilder( formateddate.format(dateNow) );
	
	/** Create scan folder (one per timepoint) */
	ScanSubFolder = "scan--"+datestring.toString();	
	(new File(ScanFolder+"/"+ScanSubFolder)).mkdir();
	TIndex = Astring.format("%1$04d",new Object[]{t});

	/** Set primary scan configuration */
	mmc.setConfig("Camera", "PrimaryScan");
	mmc.waitForConfig("Camera", "PrimaryScan");
	mmc.setConfig("Channel", channelslow[0]);
	mmc.waitForConfig("Channel", channelslow[0]);
	/** Reset ROI */
	Binning = Integer.parseInt(mmc.getProperty(mmc.getCameraDevice(), "Binning"));
	mmc.setROI(0,0,XChip/Binning,YChip/Binning);

	for (int x=0; x < NCol; x++) 
	{
		/** X filename field */
		XWellIndex = Astring.format("%1$02d",new Object[]{x});
		for (int y=0; y < NRow; y++)
		{
			/** Y filename field */
			YWellIndex = Astring.format("%1$02d",new Object[]{y});

			/** Channel loop */
			for (int c=0; c<channelslow.length; c++) 
			{
				/** channel filename field */
				CIndex = Astring.format("%1$02d",new Object[]{c});
				mmc.setConfig("Channel", channelslow[c]);
				mmc.waitForConfig("Channel", channelslow[c]);
				
				/** Compute new stage position */
				xOffset = (x * XStep)*XSign;
				yOffset = (y * YStep)*YSign;
				if(FlipXY == 1)
				{
					buf = xOffset;
					xOffset = yOffset;
					yOffset = buf;
				}
				sx = xRef + xOffset;
				sy = yRef + yOffset;
				
				/** Move stage */
				mmc.setXYPosition(xystage,sx,sy);
				mmc.waitForDevice(xystage);	
	
				for (int z=0; z < nzStepslow; z++) 
				{
					/** z filename field */
					ZSliceIndex = Astring.format("%1$02d",new Object[]{z});
				
					/** Compute new z drive position */
					sz = zOff[x][y] + (z-Math.floor(nzStepslow/2)) * zSteplow;

					/** Move z drive */
					mmc.setPosition(zstage,sz);
					mmc.waitForDevice(zstage);
					      			
					/** Check current stage position and display it */
					xPosc = mmc.getXPosition(xystage);
					yPosc = mmc.getYPosition(xystage);
					zPosc = mmc.getPosition(zstage);				
					
					if((z==0)&&(c==0))gui.message("Acquiring stack at frame " + t + " xPos " + xPosc + " yPos "+ yPosc+ " zPos " + zPosc);

					/** Capture image */
					mmc.snapImage();

					/** Copy captured image to ImagePlus structure */
					img = mmc.getImage();
					width = mmc.getImageWidth();
					height = mmc.getImageHeight();
					byteDepth = mmc.getBytesPerPixel();
					if (byteDepth == 1) 
					{
  					 ip = new ByteProcessor((int)width, (int)height);
  					 ip.setPixels(img);
					} 
					else if (byteDepth==2) 
					{
  					 	ip = new ShortProcessor((int)width, (int)height);
   				   ip.setPixels(img);
					} 
					else 
					{
   					console.message("Unknown byte depth");
					}
					
					FilePath = ScanFolder+"/"+ScanSubFolder+"/"+ImageName+"--L0000--S00--U"+XWellIndex+"--V"+YWellIndex+"--J00--E00--O00--X00--Y00--T"+TIndex+"--Z"+ZSliceIndex+"--C"+CIndex+".ome.tif";
					ImagePlus imp = new ImagePlus(FilePath, ip);

					/** Save image to file */
					FileSaver fs = new FileSaver(imp);
					fs.saveAsTiff(FilePath);
				}
			}
		}
	}

	/** End of scan message */
	out.println("XY scanfinished");
}
 /** Update time frame counter */
if(ScanMode == 1)
{
	t++;
}

gui.message("Move stage to reference...");
mmc.setXYPosition(xystage,xRef,yRef);
mmc.waitForDevice(xystage);
gui.message("Move Z drive to reference...");
mmc.setPosition(zstage,zOff[0][0]);
mmc.waitForDevice(zstage);

/** Reset ROI */
mmc.setConfig("Camera", "PrimaryScan");
mmc.waitForConfig("Camera", "PrimaryScan");
mmc.setConfig("Channel", channelslow[0]);
mmc.waitForConfig("Channel", channelslow[0]);
Binning = Integer.parseInt(mmc.getProperty(mmc.getCameraDevice(), "Binning"));
mmc.setROI(0,0,XChip/Binning,YChip/Binning);

}

/** Close connection */
gui.message("Closing socket...");
in.close();
clientSocket.close();
socketServer.close();