This page is meant for public use to share some useful collected knowledge regarding ImageJ! This notion page is a bit of an extension material for lectures at the Budapest University of Technology and Semmelweis University Ph.D. School, and it doesn’t include all the materials, just some references and extra info to help the students.
Related image processing basics presentation slides are available here:
http://cneuro.rmki.kfki.hu/education/neuroinformatics/
http://cneuro.rmki.kfki.hu/wp-content/uploads/2022/12/DIP_SOTE2022.pdf
This site also contains many links to other sites and videos, most of them on the topic of biology/medicine (e.g. https://www.ibiology.org/playlists/imaging-in-biology/), because some of the related courses.
Additional files for the practice - CT series
Table of contents
If you haven’t use earlier this software, this is an open-source Java based image processing software. You can download it from the http://imagej.nih.gov/ij website. It is a really simple software with clear menu structure, though it has a vast amount of features if you install some of its plugins. You can also try at the same place Fiji: https://fiji.sc/ the name is an abbreviation for “Fiji Is Just ImageJ”, though it’s kind of like an extended version. You can find a huge amount of use cases, help guides, and tutorials, and with the built-in sample images you can find out how can it help your research/work!
You can easily load an image or an image sequence using the File menu, but it also works in a drag-and-drop system.
This video (and you can find some more on the same channel) can help you get going via ImageJ:
https://www.youtube.com/watch?v=mzS_Ay3VT5E&list=PL1UDjbXML5Ei5aVUrFG4Wjys9jGdaeuFH
At the same channel, if you want, you can check how to create your own macros in ImageJ:
https://www.youtube.com/watch?v=4URnGkrxXP0
This way, if you need to do some steps repeatedly on different images, you can automate most of the parts, and hence you spare a lot of time! Also if you are familiar with some program languages, it worth checking how you can combine that knowledge with ImageJ! Many of our students use Matlab in their research/work/project, and you can combine it well with ImageJ: https://imagej.net/scripting/matlab
I won’t describe here the very basics, but I want to give you some highlights of some features. Let’s say you want to create a segmented image in ImageJ of an arbitrary image. You can read about segmentation in ImageJ here: https://imagej.net/imaging/segmentation
I’ll use a Scanning Electron Microscope (SEM) image as a base, to illustrate the process, and he goal would be to segment all the pores from the materials: