Image Processing on Linux

Now, what kind of work can you do with Fiji/ImageJ? One example is doing counts of objects within an image. You can load a sample by clicking File→Open Samples→Embryos.

Figure 4. With ImageJ, you can count objects within an image.

The first step is to set a scale to the image so you can tell ImageJ how to identify objects. First, select the line button on the toolbar and draw a line over the length of the scale legend on the image. You then can select Analyze→Set Scale, and it will set the number of pixels that the scale legend occupies (Figure 5). You can set the known distance to be 100 and the units to be "um".

Figure 5. For many image analysis tasks, you need to set a scale to the image.

The next step is to simplify the information within the image. Click Image→Type→8-bit to reduce the information to an 8-bit gray-scale image. To isolate the individual objects, click Process→Binary→Make Binary to threshold the image automatically (Figure 6).

Figure 6. There are tools to do automatic tasks like thresholding.

Before you can count the objects within the image, you need to remove artifacts like the scale legend. You can do that by using the rectangular selection tool to select it and then click Edit→Clear. Now you can analyze the image and see what objects are there.

Making sure that there are no areas selected in the image, click Analyze→Analyze Particles to pop up a window where you can select the minimum size, what results to display and what to show in the final image (Figure 7).

Figure 7. You can generate a reduced image with identified particles.


Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.