Using Imaris from Fiji via EasyXT-Fiji

Dear Community,

We’re happy to announce a new publicly available project by our team : EasyXT-Fiji.

Even if we prefer to rely on fully open-source solutions, Imaris has been a great tool during the past years. As we already developed a EasyXT in Matlab, we decided to go with one of our favourite tools: Fiji.

Briefly, EasyXT-Fiji will allow you to use Imaris as a minion from Fiji, for example using a groovy script you can open an imaris file, detect spots and surfaces in Imaris, get their masks of labels in Fiji, make use of your favorite ImageJ plugin and send back to Imaris additional channel and objects.

Currently, we are working on getting the API to work and stabilize, before creating ImageJ Commands that can be macro-recorded. This project is mainly intended to be used as an API when writing Groovy scripts. For that purpose, the demo folder might be the most interesting!

We’re happy to get your feedback and issues on github,

Cheers,

BIOP-IPAs

6 Likes

Hi @ThomasBoudier

@imagejan , @haesleinhuepf

We would need your opinion on the following point.

EasyXT-Fiji depends on mcib3d-core

         <dependency>
            <groupId>com.github.mcib3d</groupId>
            <artifactId>mcib3d-core</artifactId>
            <version>3.96.3</version>
        </dependency>

What would be the best practice ?

  • Ask user to add “3D ImageJ Suite”
    or
  • Upload the dependency on our own update site?

Thank you,

Romain

Hi @romainGuiet,

Thanks for including 3D ImageJ Suite in this project. Regarding dependencies usually I ask the user to install the dependency (in the case of Fiji it is quite straightforward) in order to avoid multiple versions of the same library. I also have a backup copy (if the author allows it) of a working version of the library in case something goes wrong.

In the case of 3D ImageJ Suite, you are of course allowed to get a backup of a working version. And do not hesitate to contact me if you need help using the 3D Suite library.

Best,

Thomas

2 Likes