图像降采样

原始脑片分辨率过高，与Allen平均脑模板的分辨率相差过大，为得到更好的配准效果，需要将原始脑片的分辨率降低。
😎我原本是在ImageJ软件上操作的，没想到用代码实现也并不复杂！

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package I.plugin;

import ij.ImagePlus;
import ij.gui.NewImage;
import ij.io.FileSaver;
import ij.process.ImageProcessor;

public class Test07 {
    public static void main(String[] args) {
	ImagePlus brainImage = new ImagePlus("D:/Desktop/elastix-5.1.0-win64/input/result1.tif");
	ImageProcessor bp = brainImage.getProcessor();
	int width = bp.getWidth();
	int height = bp.getHeight();
	brainImage.show();
	
	double scale = 0.1;
	int newWidth = (int)(width*scale);
	int newHeight = (int)(height*scale);
	ImagePlus resizedImage = NewImage.createByteImage("resizedImage", newWidth, newHeight, 0, NewImage.FILL_BLACK);
	ImageProcessor rp = resizedImage.getProcessor();

	rp = bp.resize(newWidth, newHeight, false);
	resizedImage.setProcessor(rp);
	resizedImage.show();
	
	new FileSaver(resizedImage).saveAsTiff("D:/Desktop/elastix-5.1.0-win64/input/resized-result1.tif");
    }
}

脑区识别

代码效果：鼠标移动到图片的哪个位置，就在Eclipse控制台输出对应的脑区，超出全脑范围则输出null。

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package I.plugin;

import java.awt.Point;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;

import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.NewImage;
import ij.io.FileSaver;
import ij.plugin.RGBStackMerge;
import ij.process.ImageProcessor;
import jxl.Cell;
import jxl.Sheet;
import jxl.Workbook;

public class Test06 implements MouseListener, MouseMotionListener {
	
	public static ImagePlus fuseImage = null;
	public static ImagePlus brainImage = null;
	public static ImagePlus annoImage = null;
	public Map<Integer,String> grayMap = new HashMap<>();
	
    // 提取脑区轮廓
	public ImageProcessor getLineImg(ImageProcessor ip, ImageProcessor op) {
		int lenX = ip.getWidth();
		int lenY = ip.getHeight();
		for(int i = 0; i < lenX; i ++) { //按列
			int begin = 0; //初始像素值为黑色
			for(int j = 0; j < lenY; j ++) {
				int temp = (int)ip.getPixelValue(i, j);
				if(temp != begin) {
					op.set(i, j, 255);
					begin = temp;
				}
			}
		}
		for(int j = 0; j < lenY; j ++) {
			int begin = 0; //初始像素值为黑色
			for(int i = 0; i < lenX; i ++) {
				int temp = (int)ip.getPixelValue(i, j);
				if(temp != begin) {
					op.set(i, j, 255);
					begin = temp;
				}
			}
		}
		return op;	
	}
	// 监听鼠标 将excel中的灰度值-脑区读取到HashMap中
	public void addMouseListener() throws Exception, IOException {
		File file = new File("D:/Desktop/rgb_name.xls");
		Workbook wb = Workbook.getWorkbook(file);
		Sheet sheet = wb.getSheet("test1");
		for(int i = 0; i < sheet.getRows(); i ++) {
			Cell[] cell = sheet.getRow(i);
			grayMap.put(Integer.valueOf(cell[0].getContents()),cell[1].getContents());
		}
//		System.out.println(grayMap);
		wb.close();
		
		fuseImage.show();
		fuseImage.getCanvas().addMouseListener(this);
		fuseImage.getCanvas().addMouseMotionListener(this);
	}
	
	@Override
	public void mouseClicked(MouseEvent e) {}

	@Override
	public void mousePressed(MouseEvent e) {}

	@Override
	public void mouseReleased(MouseEvent e) {}

	@Override
	public void mouseEntered(MouseEvent e) {}

	@Override
	public void mouseExited(MouseEvent e) {}
		
	@Override
	public void mouseDragged(MouseEvent e) {}

	@Override
	public void mouseMoved(MouseEvent e) {
		// 监听鼠标的移动
		int currentSlice = fuseImage.getCurrentSlice();
		Point point = fuseImage.getCanvas().getCursorLoc();
		int val = (int)annoImage.getImageStack().getVoxel(point.x, point.y, currentSlice-1);
		
		System.out.println(grayMap.get(val));
	}
	// 主程序
	public static void main(String[] args) throws IOException, Exception {
		brainImage = new ImagePlus("D:\\Desktop\\elastix-5.1.0-win64\\input\\result1-1.tif");
		ImageStack brainStack = brainImage.getStack();
		
		annoImage = new ImagePlus("D:\\Desktop\\elastix-5.1.0-win64\\result\\result.tif");
		ImageProcessor ap = annoImage.getProcessor();
		int width = ap.getWidth();
		int height = ap.getHeight();
		
		ImagePlus lineImage = NewImage.createByteImage("lineImage", width, height, 0, NewImage.FILL_BLACK);
		ImageStack lineStack = lineImage.getStack();
		ImageProcessor lp = lineImage.getProcessor();
		
		ImageProcessor op = new Test06().getLineImg(ap, lp);

		lineImage.setProcessor(op);
		lineImage.show();
 		
		fuseImage = NewImage.createByteImage("fuseImage", width, height, 0, NewImage.FILL_BLACK);
		
		ImageStack fuseStack = RGBStackMerge.mergeStacks(brainStack, lineStack, null, true);
		fuseImage.setStack(fuseStack);
		new FileSaver(fuseImage).saveAsTiff("D:/Desktop/fuseImage-1.tif");
		
		new Test06().addMouseListener();
	}
}

操作演示

操作演示

注意事项

  1. Eclipse中导入jxl.jar包，具体方法可参考博客，需要注意jxl.jar包只能处理.xls文件
  2. 脑片降低分辨率后统计出的各个脑区的细胞数目，需要与人工计数的结果进行对比，如果差别不大，则后续采用降低分辨率的脑片进行配准。
  3. 配准后的图像使用Imaris软件计数，具体操作步骤见文章Imairs细胞计数教程

参考文章