Bio-Formats

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Bio-Formats features in ImageJ and Fiji

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Note

This documentation is for the new Bio-Formats 5.1 version. See the latest Bio-Formats 5.0.x version or the previous versions page to find documentation for the version you are using.

Fiji overview

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

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.

Using Bio-Formats daily builds

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.

Warning

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.

Manual upgrade

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.

  1. Fiji must first be fully updated
  2. Close Fiji
  3. Open the Fiji installation folder (typically named ‘Fiji.app’)
  4. Remove bio-formats_plugins.jar from the ‘plugins’ sub-folder
  5. Remove all of the .jars from the ‘jars/bio-formats’ sub-folder:
    • jai_imageio.jar
    • formats-gpl.jar
    • formats-common.jar
    • turbojpeg.jar
    • ome-xml.jar
    • formats-bsd.jar
    • ome-poi.jar
    • specification.jar
    • mdbtools-java.jar
    • metakit.jar
    • formats-api.jar
  6. Download bio-formats_plugins.jar (from the latest release http://downloads.openmicroscopy.org/bio-formats/) and place it in the ‘plugins’ sub-folder
  7. Download each of the following (from the latest release http://downloads.openmicroscopy.org/bio-formats/) and place them in the ‘jars/bio-formats’ sub-folder:
    • jai_imageio.jar
    • formats-gpl.jar
    • formats-common.jar
    • turbojpeg.jar
    • ome-xml.jar
    • formats-bsd.jar
    • ome-poi.jar
    • specification.jar
    • mdbtools-java.jar
    • metakit.jar
    • formats-api.jar
  8. To Check Version of Bio-Formats Select Help > About Plugins > Bio-Formats Plugins... Check that the version of Bio-Formats matches the freshly downloaded version.
  9. Start Fiji and open any Image file using Plugins > Bio-Formats > Bio-Formats Importer

Note

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.