Fiji is an image processing package. It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Fiji works with Bio-Formats out of the box, because it comes bundled with the Bio-Formats ImageJ plugins.
For further details on Bio-Formats in Fiji, see the Bio-Formats Fiji wiki page.
Upgrading Bio-Formats within Fiji is as simple as invoking the “Update Fiji” command from the Help menu. By default, Fiji even automatically checks for updates every time it is launched, so you will always be notified when new versions of Bio-Formats (or any other bundled plugin) are available.
Fiji currently shipping with the 5.1.x release versions of Bio-Formats. However, if you have encountered a bug which has been fixed by the Bio-Formats team but not yet released, you can use the Bio-Formats update site to access the daily build as described in the Fiji documentation.
These builds are not yet released and should be considered beta in quality. In particular, you should avoid exporting data using the Bio-Formats Exporter in case you write incompatible files which cannot be read by released versions of Bio-Formats or other OME-compliant tools.
We recommend waiting for a fully tested release version of Bio-Formats if possible.
Manually updating your Fiji installation should not be necessary but if you need to do so, the steps are detailed below. Note that although we assume you will be upgrading to the latest release version, all previous versions of Bio-Formats are available from http://downloads.openmicroscopy.org/bio-formats/ so you can revert to an earlier version using this guide if you need to.
It is vital to perform all of those steps in order; omitting even one will cause a problem. In particular, make sure that the old files are fully removed; it is not sufficient to add the new files to any sub-directory without removing the old files first.