FIJI versus ImageJ2 or ImageJ

Recently I’ve started using FIJI. Works well. However I hear that there are such variations called ImageJ2.
What is real fundamental difference of ImageJ2 when you compare it with FIJI and/or ImageJ?

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Well, Fiji Is Just ImageJ, as it is ImageJ2 with plugins, and this includes ImageJ1 with a compatibility layer. See the ImageJ page for details.

got it. there is no fundamental difference.

Hi @1timur1

Just to clarify again. There is a fundamental difference between ImageJ v1.x and ImageJ2/Fiji, as the latter is a complete rewrite of the former. That legacy layer to which @imagejan refers was to preserve backwards compatibility so that old-style plugins/macros can still run.

You can always read even more details about ImageJ2 and all the goodies it brings here… ImageJ2: ImageJ for the next generation of scientific image data.

eta :slight_smile:


Hi all,

So is the last and best version to download FIJI or ImageJ2?



Good day Chloë,

with FIji you are mostly on the save side. If you prefer slim software, have a look at plain ImageJ.



great thank you Herbie!


Fiji is ImageJ2. Ok - I know … this is a bit confusing - but you can read up on the ‘flavors of ImageJ’ here.

Fiji is just ImageJ2 (plus the legacy layer for ImageJv1.x-compatibility) - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. In general, we recommend downloading/using Fiji.

eta :slight_smile:

Just starting with ImageJ and seriously confused. Nowhere you can find information on the actual differences.

Why would anyone keep updating ImageJ1 (in fact it appears to be updated more frequently than Fiji, at the very least with stable public releases, Fijis latest one is almost TWO FRICKING YEARS OLD!)? Why not have ONE piece of software that includes everything someone might need? Is there anything in ImageJ1 that is not in ImageJ2? Or vince versa? If so, what is the excuse for the other piece of software not to include that new feature?

I can’t really understand the “use ImageJ1 if you like slim software” argument. One or more software developers invest countless hours of precious time into it. Software is preferrably slim, but why choose an inferior piece of software just because it’s “slimmer”? Nobody is running this on a 20 year old machine anyway, saying “oh well, looks like I can only use the inferior ImageJ1 because I can’t be bothered updating to a machine only 15 years old I found on craigslist for free”.

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Completely agree! ImageJ, ImageJ1, ImageJ2, ImageJFX, Fiji, Java 6 to 8 transition and dates of newest releases are very confusing. This is not the first time I installed ImageJ and I still have no clue what is in active development and most modern. “Flavors of ImageJ” link doesn’t help much. After reading it, I assumed ImageJ2 is most modern, but jumping to its page, the first thing I see is Java 6 to 8 transition issue. Recommended Fiji is not at the top of the table, but hiding in the 4th row. ImageJFX, the newest kid on the timeline, seems to be dead, but is listed as actively developed.

It took me couple of hours of link hopping to make sure that Fiji is the way to go.

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I understand that this ecosystem is sometimes very hard to access. I also don’t mean any offence now. But the ImageJ website can be edited by users like me or you.

There is no one payed to do sales, advertisement, marketing or management here. It is just us who can make Fiji/ ImageJ better and more accessible.

Just my two cents :wink:

EDIT: to exemplify this, I put Fiji in the list on top. (Please no one crucify me on this one :dizzy_face:)

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My comment was just a feedback from frustrated user, nothing personal towards all developers who made this very useful piece of software.

I had no idea that I can edit the website. Where is the repository? I’ve seen various ImageJ related repositories on GitHub, but not the website. Is it done through ImageJ Wiki?

No problem, I understand where it comes from :slight_smile:

Just create an account:

Then you can edit it just like a wiki. In the upper right corner there is a button “edit” once you are logged in:


Then you can edit it just like a wiki:

I use both ImageJ 1.x and Fiji and by far prefer the former. It loads and runs much faster and is much simpler to use for a non-programmer, since you can just use the “Compile and Run” feature for plugins without any need to learn or understand an code-management system.

Also, most of the plugins in Fiji were written for bio-sciences and have limited usefulness outside that field. I work with materials technology, so I prefer to develop my workflow in ImageJ 1.x, and rather move the few plugins I need from Fiji over to my ImageJ 1.x based installation. Nearly everything that works in Fiji will also work in ImageJ 1.x if you use Java 8 and include the dependency libraries. That goes the other way too; nearly everything you develop for ImageJ 1.x will also work in Fiji. So there is really not any need to choose any fixed path; just use the solution that fits your workflow best, and you can change it later. Both platforms are very flexible.

Regarding updates, if you download a couple of years old Fiji installation you can just use the built-in updater for the plugins you need, also for the ImageJ 1.x layer. So it really does not matter much how old the core installation is, as it can be updated online.


In my 15 minutes of experience with Fiji, adding plugins involved a few clicks and Manage Update Sites dialog. Are there plugins, which can’t be added this way?

I meant for writing your own custom plugins using code examples found elsewere, or recompiling existing code. Yes installing existing plugins is easy in Fiji. But often they do not fit your need exactly, you must then change the code and recompile. That is super-easy in ImageJ 1.

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