Installing Bio-Formats in ImageJ

Note

Since FIJI is essentially ImageJ with plugins like Bio-Formats already built in, people who install Fiji can skip this section.

If you are also using the OMERO plugin for ImageJ, you may find the set-up guide on the new user help site useful for getting you started with both plugins at the same time.

Once you download and install ImageJ, you can install the Bio-Formats plugin by going to the Bio-Formats download page.

For most end-users, we recommend downloading the bioformats_package.jar complete bundle.

However, you must decide which version of it you want to install. There are three primary versions of Bio-Formats: the latest builds, the daily builds, and the release versions. Which version you should download depends on your needs:

• The latest build is automatically updated every time any change is made to the source code on the main “dev_5_0” branch in Git, Bio-Formats’ software version control system. This build has the latest bug fixes, but it is not well tested and may have also introduced new bugs.
• The daily build is a compilation of that day’s changes that occurs daily around midnight. It is not any better tested than the latest build; but if you download it multiple times in a day, you can be sure you will get the same version each time.
• The release is thoroughly tested and has documentation to match. The list of supported formats on the Bio-Formats site corresponds to the most recent release. We do not add new formats to the list until a release containing support for that format has been completed. The release is less likely to contain bugs.

The release version is also more useful to programmers because they can link their software to a known, fixed version of Bio-Formats. Bio-Formats’ behavior will not be changing “out from under them” as they continue developing their own programs.

Note

There are currently two release version of Bio-Formats as we are maintaining support for the 4.4.x series while only actively developing the new 5.x series. Unless you are using Bio-Formats with the OMERO ImageJ plugin and an OMERO 4.4.x server, we recommend you use Bio-Formats 5. A new 4.4.x version will only be released if a major bug fix is required.

We often recommend that most people simply use the latest build for two reasons. First, it may contain bug-fixes or new features you want anyway; secondly, you will have to reproduce any bug you encounter in Bio-Formats against the latest build before submitting a bug report. Rather than using the release until you find a bug that requires you to upgrade and reproduce it, why not just use the latest build to begin with?

Once you decide which version you need, go to the Bio-Formats download page and save the appropriate bioformats_package.jar to the Plugins directory within ImageJ.

Plugin Directory for ImageJ: Where in ImageJ’s file structure you should place the file once you downloaded it.

You may have to quit and restart ImageJ.  Once you restart it, you will find Bio-Formats in the Bio-Formats option under the Plugins menu:

You are now ready to start using Bio-Formats.