Image Processing on Linux

Figure 8 shows an overall look at what was discovered in the summary results window. There is also a detailed results window for each individual particle.

Figure 8. One of the output results includes a summary list of the particles identified.

Once you have an analysis worked out for a given image type, you often need to apply the exact same analysis to a series of images. This series may number into the thousands, so it's typically not something you will want to repeat manually for each image. In such cases, you can collect the required steps together into a macro so that they can be reapplied multiple times. Clicking Plugins→Macros→Record pops up a new window where all of your subsequent commands will be recorded. Once all of the steps are finished, you can save them as a macro file and rerun them on other images by clicking Plugins→Macros→Run.

If you have a very specific set of steps for your workflow, you simply can open the macro file and edit it by hand, as it is a simple text file. There is actually a complete macro language available to you to control the process that is being applied to your images more fully.

If you have a really large set of images that needs to be processed, however, this still might be too tedious for your workflow. In that case, go to Process→Batch→Macro to pop up a new window where you can set up your batch processing workflow (Figure 9).

Figure 9. You can run a macro on a batch of input image files with a single command.

From this window, you can select which macro file to apply, the source directory where the input images are located and the output directory where you want the output images to be written. You also can set the output file format and filter the list of images being used as input based on what the filename contains. Once everything is done, start the batch run by clicking the Process button at the bottom of the window.

If this is a workflow that will be repeated over time, you can save the batch process to a text file by clicking the Save button at the bottom of the window. You then can reload the same workflow by clicking the Open button, also at the bottom of the window. All of this functionality allows you to automate the most tedious parts of your research so you can focus on the actual science.

Considering that there are more than 500 plugins and more than 300 macros available from the main ImageJ website alone, it is an understatement that I've been able to touch on only the most basic of topics in this short article. Luckily, many domain-specific tutorials are available, along with the very good documentation for the core of ImageJ from the main project website. If you think this tool could be of use to your research, there is a wealth of information to guide you in your particular area of study.

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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.