Integration of Fiji / "Image Suites" in electronic lab notebooks

Hi here,

Does anybody have experiences integrating Fiji/ImageJ with electron lab notebooks (ELN) / repositories?

Ideally you end up automatically with an entry in the lab book, when you are done using a macro/script (which might reside in git) in order to document, what happend when with which parameters. Goal is to facilitate reproduction of results. Background is the discussion in Germany about the rules for good scientific practise (gsp) in order to document provenance of images.

Sure there might be an API to put information into an ELN, but before I start going into this direction I am looking for opinions on the topic.

Note: I am not looking for jupyter notebooks or alike. Although the state of an executed notebook could also go into en ELN.


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Hey Stephan

I’m not sure how many folks here are familiar with which ELNs are worth considering. Perhaps if you could recommend a few ELNs, then some of the ambitious folks from the IJ community would start putting something together.

I know @axtimwalde was messing around with the ELN named “ELN” which seems nice but may not be as full featured as some folks would need. I know one thing that bothered me about it was that you can’t embed videos.


Thanks for reply Kyle! uses It features simple but powerful UI which helps with the adoption. Our IT coordinator evaluated at least 5 ELNs. It’s really hard to recommend the right one, because of different needs/circumstances.

And before putting something together I would rather research the current state.

I could also rephrase the question into: How do people do image provenance? How do they keep track of image manipulation/analysis in order to reproduce a result.


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