Best way to process Image Sequence


I have an Image Sequence that I generated via Fiji.
I’m currently developing a plugin, and I need to access various properties of the stack and creating new stack, i.e. standard deviation and mean stacks.

I’m confused, what is the best way to solve this in Java? using dataset, ImgPlus, ImagePlus?


Hi @yarinbehere,

Welcome to the forum.

Is the Image Sequence something your plugin will assume is already open in Fiji? Or is the expectation that these are files that the plugin itself will have to open from files?

I’m not sure there’s a “best” way, since you can do this both Dataset/ImgPlus, or ImagePlus.
But Dataset/ImgPlus use some newer, nicer infrastructure, so I’d recommend going with those unless there is ImageJ1 stuff you know you’ll need.

Have you seen the different web pages about scripting in Image?
Those would be a good place to start:

There are other resources too.


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Thanks John,
Are there any key differences between Dataset and ImgPlus?

I assume the user selected a folder with .tif images, created Image Sequence and saved it on his local machine (I’ll develop that part in the future, using service or in alternative way, as far as I concern).
The plugin opens the file (hard coded, meanwhile) and stars to work.


Hi Yarin (@yarinbehere),

Not really, a Dataset is an ImgPlus but with extra stuff:

Dataset is the primary image data structure in ImageJ. A Dataset wraps an ImgLib ImgPlus . It also provides a number of convenience methods, such as the ability to access pixels on a plane-by-plane basis, and create new Datasets of various types easily.


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