ScientiFig v3.01: images deleted instead of landing on image list

Tags: #<Tag:0x00007fd53e519008>


I love using the ScientiFig plugin but lately I have trouble with sending back images to the image list. Instead, they just get deleted. This happens if the images come from other ScientiFig .yf5m files, or crops from ROIs I created. This is annoying because I cannot use these crops then to make their own panels, they come up as individual images.

Is there a way around this? Any help will be greatly appreciated.


I invited the developer of ScientiFig, Benoit Aigouy (, to this topic (using the Invite button). Maybe he can help here…


Dear @norafekete,

thanks for using our tool. I think the problem comes from original image files being moved (or deleted from the hard drive by the user). It is true that the yf5m file embeds original images (to avoid the path issues mentioned before), but it only does so when images belong to a panel or a figure. However, images are not embedded (they are instead directly read from the drive) when they are removed from a panel and sent back to the original list. In the latter case, if the original image file does not exist anymore or if its path has been changed, then the image is simply deleted from the original list. I did choose this for various reasons when I coded the tool, but maybe this was a wrong choice, I’ll see if I can think of a quick workaround or if I think of a code fix to avoid these issues and I’ll do my best to keep you posted in a few days.



@imagejan thanks for letting me know, I would have missed this post without your help.



the issue you mentioned should now be fixed if you update your FIJI and restart. From SF V3.1 onwards, missing/moved images and crops can be sent back to the image list instead of being discarded (please note however that they are actually just kept in memory only as long as SF runs and they will be forever lost/discarded if you close SF/FIJI/java while they are in the image list, in other words images must belong to a panel or a figure to be saved in the yf5m file). Please let me know you if you still experience some problems or discover new issues (for the record, I had to modify big chunks of my code to fix the issue you reported, a process that is always at high risk…).




Thanks @baigouy for the quick response!

I saw that the ScientiFig update site ships a new version now, but I couldn’t see any changes on the github repository:

Is that repository supposed to contain the latest source code, or do you host your code somewhere else now?


@imagejan just updated the github repo (something I hadn’t done in a while).


Yes, thank you @baigouy, after the update every image lands on the image list. Thanks!