This system is a plugin for ImageJ software that can stitch multiple microscopy images in X and Y axis using pixel matching and position understanding. We will need to follow the steps mentioned below to get it to work:
We will first need to download the latest version of ImageJ software from the official website (https://imagej.net/Downloads). Once we have installed the software, we will create a new plugin project and name it "Image Stitcher".
Next, we will need to import the necessary libraries for our plugin. We will need the following libraries: 'ij.', 'ij.process.', 'java.awt.', and 'java.util.'. These libraries will allow us to access the ImageJ API and perform image processing operations.
The plugin will prompt the user to select multiple images to stitch together. The images can be loaded using the 'ij.io.Opener()' method. Once the images are loaded, we will need to convert them to 'ImageProcessor' objects to perform further image processing.
We will need to determine the overlap between the images to stitch them together. To find the overlap, we will use a method called pixel matching. This involves finding the matching pixels in the overlapping regions of the images. We will use the 'ij.process.ImageStatistics' class to compare the pixel values of the images and find the matching pixels.
Once we have found the matching pixels, we will need to calculate the position of each image relative to the others. We can use the coordinates of the matching pixels to calculate the position of each image. We will store the position of each image in a 'HashMap object'.
After we have found the position of each image, we can use the 'ij.ImagePlus' class to create a new image that is the size of all the images combined. We will then copy each image into the new image at the correct position using the 'ImageProcessor's insert()' method.
Once the images are stitched together, we will need to save the final image. We can use the 'ij.io.FileSaver' class to save the image as a TIFF or JPEG file.
Note :
The 'findOverlap' method takes two 'ImageProcessor' objects as input and tries to find the overlapping region between them. It does this by comparing the pixels in the overlapping region of the two images and looking for regions where the pixel values are similar. The method uses the 'ImageStatistics' class to get the minimum and maximum pixel values for each image and then sets a threshold for how different two pixels can be and still be considered a match. It starts by checking the maximum possible overlap between the two images and works its way down, trying to find the largest overlapping region where the pixels match. If it finds an overlap, it returns the position of the overlap as an array of two integers, where the first integer is the width of the overlap and the second integer is the position of the right edge of the overlap in the first image. If it does not find an overlap, it returns 'null'.