Which Fiji plugins should be featured on the front page?

An effort has begun to update the https://fiji.sc web site to the latest web standards:

One remaining question is what to do about the carousel currently on the front page. It highlights several plugins, but the content of the carousel has not been updated in years. We would like to update it to feature Fiji plugins that are currently awesome, noteworthy, useful, etc., now in 2019.

Some of the currently featured plugins like TrakEM2 and Simple Neurite Tracer remain incredibly useful and should continue to be highlighted. But there are a slew of newer plugins that are not mentioned on the front page, but should be: BigDataViewer, BigStitcher, SciView, and many others.

Therefore, I start this topic! Let’s make the list as a community. :sunny: Respond to this post with your favorite, most useful Fiji plugin deserving of a front-page blurb! Please include:

  1. Name of the plugin—which must have a page on https://imagej.net/, and must be accessible as part of Fiji or from an ImageJ update site.
  2. One sentence, or sentence fragment, describing a use case of the plugin.
  3. Plain screenshot of the plugin doing its thing. (The current version of the site has the screenshots fed through a fancification process—we won’t do that anymore, in favor of keeping it as easy as possible to add more featured plugins as time goes on.)

See the current https://fiji.sc front page for inspiration.

Then as a community, we can upvote replies here for plugins we agree should be featured. We’ll add any Fiji plugin achieving 5+ likes! :electric_plug: :+1: :heart:


Manual tracking by @Fabrice_Cordelieres
For when you need to see how much something moves, and how often. Super helpful if you think computers are idiots, and you can do a better job. I used it, its an intuitive, simple program to use, and very, very helpful.

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Please note that the Manual Tracking plugin (authored originally by @Fabrice_Cordelieres) has nothing to do with TrackMate by @tinevez (except that both are included in Fiji, of course ; )


CLIJ is a plugin for GPU-accelerated image processing offering about 100 predefined OpenCL-based functions allowing you to run your workflows on any GPU.


Here is a non-exhaustive list of plugins and plugin suites I would love to see featured on fiji.sc. Some of these have separate update sites, so aren’t “Fiji plugins” per se, but well worth highlighting regardless:

note: strike-through plugins are posted below

But I don’t have time to make up screenshots and blurbs for them all. :frowning_face: Could others please help? It doesn’t have to be a plugin you authored or maintain (although it can be)—just a plugin you value, and for which you are comfortable making a nice screenshot + use case blurb.


The Microscope Image Focus Quality Classifier predicts an absolute measure of image focus on a single image in isolation, without any user-specified parameters. It uses a pre-trained deep neural network, operating at the image-patch level, and also outputs a measure of prediction certainty, enabling interpretable predictions.

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Wow, this is already a lot of information! If the number of plugins is rather large, what I can do is create a .json file (or some other iterable object) that stores the data for each of these plugins, and then generates the resulting card/tab/whatever container for each of the mentioned plugins. Then, we could incrementally showcase plugins rather simply.

(“in theory” this is what React/Angular/Vue/Backbone/etc. is supposed to be for, but if it’s for something comparatively simple I can probably just use jQuery and be fine with it).

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It’s true. Maybe we should limit the use case blurbs to one sentence or fragment of phrase? What do you think?

Sounds great. Should make PRs against the website repository easier for non-technical folks—they can just copy/paste a new line into the JSON and hack the contents, right? I think the trickiest thing is where to host the screenshot images. Are you OK with a mixture of local and remote images? Or should we always commit them to fiji.github.io?

I don’t mind having longer blurbs, as long as users are alright with maintaining them (i.e. sending in a PR). And yes, it should make the PRs easier for non-technical users, especially since they can just edit the JSON file in GitHub’s web editor (no need to download Git, use a text editor, etc.).

I moved some of the images that you used for the partnered objects locally, both to run some image compression algorithms and to help with the amount of requests we make (and to where). However, it’s also fine to use external links.

Big thing is that I’d have to make sure that the inputs are sanitized, but I can definitely do that!


I would add


ah, yeah, good point, I will correct that

SIMCheck (@graemeball), used daily no Fiji page but update site

Naturally we are deeply impressed with 3Dscript, published in Nat Methods April 2019 and we recieved so many (in the thousands) of lovely feedback on Twitter already and > 1.000 downloads from https://github.com/bene51/3Dscrip within just three weeks…
So please if ye like it…


Based on past experience: I am only interested in promoting ImageJ and Fiji extensions that are well-maintained. SIMcheck and 3Dscript would be great functionality to feature, but they need ImageJ wiki pages first. Since it is a wiki, anyone in the community could create such pages—but either way, a commitment from the authors (@carandraug and bene51) to support these plugins is vital to the community.

I filed issues in the respective issue trackers:



morphological data mining, three-dimensional modeling, image stitching, registration, editing, and annotation

@albertcardona @axtimwalde



Simple and efficient alignment of multi-tile and multi-angle image datasets

@StephanPreibisch @hoerldavid



bone image analysis, including tools for trabecular geometry and whole bone shape analysis


@mdoube @alessandrofelder


Coloc 2

pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing





morphological filtering and reconstruction, watershed segmentation, 2D/3D measurements, and binary/label images utilities.





3D visualization and virtual reality capabilities for images and meshes


@kephale @skalarproduktraum