N5 plugins for Fiji

Together with our manuscript about large scale cellular organelle reconstruction from FIB-SEM at 4 and 8nm isotropic resolution https://www.biorxiv.org/content/10.1101/2020.11.14.382143v1 we released Fiji plugins to open and save N5 compatible formats (N5 filesystem, Zarr, HDF5, N5 AWS S3, N5 GoogleCloud) in Fiji. The plugins are distributed with the main update site, i.e. next time you update, you got it.

You can now open datasets or crops of datasets in Fiji (File > Import > N5), save images as datasets (File > Save As > Export N5) or you can view them with BigDataViewer (Plugins > BigDataViewer > N5 Viewer). The ImageJ plugins open individual datasets or crops, the BigDataViewer plugin open individual datasets, and multi-scale and multi-channel groups.

Check this screencast for a teaser how to access our public OpenOrganelle data.


More details, instructions, tutorials on the n5-ij github page:

Some short demos: