Use GitLab scripts in Fiji

Dear all,

I am doing fluorescence image analysis and I want to use a segmentation method that is available on GitLab to segment my cells in Fiji. So far I have only worked with tools and plugins available in ImageJ and wrote some macros for automation. However I have never used GitLab scripts, which is why I have no idea on how to use them. The method is available under

and described in this paper:

https://www.frontiersin.org/articles/10.3389/fnana.2019.00081/full

Can someone explain how to use it?

Thanks a lot,

Best regards!

Hi @MonaF,

I had a quick look at the script and I’m pretty sure this isn’t a Fiji-compatible script collection. Did you try to contact the authors?

Cheers,
Robert

Hi Robert,

thanks, I thought so too. In Phython 2 the script can be run. No I didn´t contact the authors.

Best,

Mona

If you change the headline of your post to what you want to do (instead of Fiji and gitlab, which are unrelated), you can increase the likelihood that some expert from the right field reads your post and can help you.

By sharing some example images you give us the chance to tell you what alternate tools could be used to process your data.

Furthermore, contact the authors of these scripts, they know for sure how to use them :wink:

Cheers,
Robert

Hi Mona, as Robert mentioned, the script uses Python modules (PIL, numpy) that are not accessible via the python shipped with fiji (so called Jython).
The Jython shipped has the python standard library (os…) but for other functionalities Fiji/Java libraries are used.

You are right, thanks for the advice! :slight_smile:
This post was more about how to use python scripts in general in Fiji and I did not aim for a specific mehtod, which is why i did not include example images. And I was confused about which python script I should use because there are so many in the GitLab link.

But, if it can not be run in Fiji, the question is solved anyway. :smiley:

Best,
Mona

Hi Thomas,

thank you! :slight_smile: