EasyFiji: A Graphical Interface for User-Friendly Fluorescence Image Processing in Fiji

If you ever use Fiji, you know how powerful it is and how quickly you can get lost in all these menus and settings. EasyFiji takes the stress out of image processing with simple buttons, sliders, and smart tools that just work. It's Fiji but friendly.

The recommended way to install EasyFiji is through the Fiji update site. Just click the help, update, click manage update site and type EasyFiji. Remember to click this and click apply and close.

Apply changes, then restart EasyFiji. Advanced users could also choose to download the JAR files from the GitHub webpage. For the color channel adjustment, we can open any multi-channel images, and using the channel color tab, we can choose different lookup tables here.

We can choose red, green, blue, extra, or we can choose the black one to disable the specific channel. We can use all channel to show all the channel colors, or we can use each channel to display only a specific channel. For the gain sliders, we can make the images brighter.

If the image is too dark, we can make this brighter. And for the offset one, we can set the minimal intensity on the image. So we can adjust all the channels'color or only specific channels.

For the channel view, open the image of interest. This one is a multi-channel images. So each individual channel have different intensities and a location.

For the Colocalization button, it will create the RGB images by using two channels. It will highlight regions where both channel have similar intensities by displaying in those pixels in yellow. The FFMerge button also combines two channels into a RGB display but in a different way.

Here, each channel remains equally visible. This make overlapping regions easier to interpret without losing channel balance. The FGMerge button overlays one or more channels onto a green scale channel.

It is useful when combining with green scale images like DIC or EM.channels are preserved by the green scale channel size, overall contrast can give you a much better image quality. Here is another example images using FGMerge. For the stack views, the EasyFiji plugin provides function like maximum intensity projection, orthogonal slice views, and the kymograph.

Image processing tab. Open an image, click the record button to start recording command. The smooth function will apply a Gaussian blur, and the denoise function will apply a Median filter, and the sharpen button will apply 2D unsharper mask, and subject background will apply the rolling ball signal, rolling ball algorithm to remove background.

And applied look up table will change the, will apply the gain and offset as specified in the display panel. Here we could see, like, after applying this processing command, we could see, like, the image quality gets much better. Here I will show example of using Local Correction button to apply a correction factor so that the medium intensity of each frame becomes local to the value of the fit curve.

Local and global correction can be applied sequentially to the same dataset. Here it shows the intensity profile before and after bleach correction. We could see that the signal has been corrected.

Here we show different saving options. The save panel is use-case orientated to a non-expert in selecting the correct file format for their use. We can save the images as a raw dataset.

It will contain all the image's informations. We can save as JPEG for presentation, or we can save the images as PNJ format. And we can also save the image stack as movies.

The image info panel, this panel display vendor-specific acquisition metadata in a human readable way for images acquired thus. After this video, you should have a good understanding of how to use this plugin to visualize and processing biomedical images. Our purpose to develop EasyFiji is to make image analysis easier, faster, and more accessible for life scientists.

Whether you are charting contrast, applying filters, or exploring image metadata, EasyFiji is here to make your work with Fiji smoother and more enjoyable.