ImageJ is Java-based image processing software developed by NIH. It is used as standard in biological research.
Since ImageJ is open source, there are many distributions, especially Fiji. That's why it's called "Fiji is just ImageJ". When you think "I want to do this kind of processing" in image analysis, Fiji has most of the functions. (However, advanced ones are excluded. Let's implement advanced ones in MATLAB or Python.)
The basic functions for using ImageJ are summarized below.
For example, if you take a video, ImageJ will load it as a collection of multiple images. In the case of saving, if it is in tif format, multiple images can be saved as one set (stack) in one file. As a stack, there is a connection in the time axis direction like a movie, but there are other stacks when the depth (z direction) is changed (that is, a stack made by slicing 3D data) and RGB. There is a connection (channel) due to the difference in wavelength. In ImageJ, these three connections can be separated into a stack, and a hyper stack that can be up to 5D information can be handled. Hyper stacks can also be saved as tif files. However, if you read this with MATLAB etc., the 5D stack will also be read as 3D. The order is channel, z stack, and time stack.
LookUp A common task is to linearly convert the brightness with Brightness / Contrast under Ajust on the Image tab. You can also change the color with Look Up tables. The point is that ** the brightness value of the image is not changed at all ** because LookUp only changes the appearance. I'm just changing the display method. If you look at the saved one with other software, it may not change at all. However, when you press the [Apply] button, the appearance is adopted and the brightness value changes.
ROI(region of interest) It is a function to specify the area of the image and mark it, and set the pixel as the area of interest. For stacked images, you can also specify and mark slices. The square and circle buttons are the settings for how to take the ROI. You can register the ROI enclosed by the [crtl key + t] command in the ROI maneger. [Measure] displays the information for the area. ROIs can be attached to images as overlays and can be saved as a separate roi file from the image.
You can also set meta information such as the length per pixel (that is, resolution), and save it in the tif file format. Information can be found in [Properties ...] and so on. You can also add a scale bar with [Scale bar ...] based on this length information.
A macro is a function that records and automates a series of processes. Recording starts with [Record ...] of [Macros] of [Plugin], and then the processing you have done is recorded. It's similar to an Excel macro and is very useful. Macros can be saved as ijm files.
plugin It's similar to a macro, but it's a feature that allows you to extend the functionality of ImageJ. Many plugins are introduced on the ImageJ homepage. Put the jar file (compiled java executable file) in the plugin folder and it will be installed. You can also develop your own plugin and write it in Java.
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