Writing about using Fiji software in research



Hi everyone,

I want to write that I used Fiji in my research, usually when we write that we use a material or equipment we need to write the following information after ( the material name, the company that provide it and the country of origin). Should I do the same when I write about using Fiji and if the answer is yes what should I write?

Thank you.


Welcome to the forum, @Sana1!

Depending on what components/plugins you used, you should cite one or several of the publications as listed on the Citing page in the ImageJ wiki:


Yes I know about the citation and I will do it. I am asking about what should I write after mentioning that I used Fiji . Thank you.


You can take a look at examples of how others have done this in the literature. For example:

where Fiji and ImageJ are cited as follows:

The software for training the model and making predictions is open source and the pre-trained model is available for download and use in both Fiji (ImageJ) [19, 20] and CellProfiler [21].

[19] Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods. 2012;9:671–5.
[20] Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J-Y, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–82.

How you format this will depend on the preferences of your target journal.


There is also something to be said about documenting the version number, but that gets a little complicated with Fiji (I think?).


I think I got it now, citation is all what I need.
Thank you so much