BIRDS plugin for FIJI


Has anyone else tried the BIRDS plugin for FIJI to register whole mouse brain images to the Allen Brain Atlas? GitHub - bleach1by1/BIRDS_plugin: BIRDS plug-in on Fiji and attached jar package

My experience with the test datasets has been that only some of them are able to be processed. For the ones that don’t, FIJI gets hung up after the first downsample step. Several blank windows pop up that are impossible to close and clicking “ok” does nothing. At this point FIJI cannot be closed without ending the task in the task manager.

For the test datasets that work, the registration is very accurate and the manual correction feature is quite helpful. However, for the final visualization/quantification step using Imaris, it seams that a very powerful computer with a Windows OS is necessary as the program becomes unresponsive after several minutes on a computer with 96GB RAM. We have access to a research computing facility, but it runs on Linux.

Using our own dataset we cannot get past the first step as the “hang-up” and blank error windows inform us of nothing that might help better understand the problem. If anyone has any ideas for troubleshooting please reply.



Not heard about this one unfortunately.

Perhaps it would be interesting to point the maintainers of BIRDS to this post as well as the one trying to reference the archipelago of brain registration tools available.


I contacted the developers and they fixed a bug which solved the problem.