Bio-Formats features in ImageJ and Fiji

When you select Bio-Formats under the Plugin menu, you will see the following features:

  • The Bio-Formats Importer is a plugin for loading images into ImageJ or Fiji. It can read over 140 proprietary life sciences formats and standardizes their acquisition metadata into the common OME data model. It will also extract and set basic metadata values such as spatial calibration if they are available in the file.

  • The Bio-Formats Exporter is a plugin for exporting data to disk. It can save to the open OME-TIFF file format, as well as several movie formats (e.g. QuickTime, AVI) and graphics formats (e.g. PNG, JPEG).

  • The Bio-Formats Remote Importer is a plugin for importing data from a remote URL. It is likely to be less robust than working with files on disk, so we recommend downloading your data to disk and using the regular Bio-Formats Importer whenever possible.

  • The Bio-Formats Windowless Importer is a version of the Bio-Formats Importer plugin that runs with the last used settings to avoid any additional dialogs beyond the file chooser. If you always use the same import settings, you may wish to use the windowless importer to save time (Learn more here).

  • The Bio-Formats Macro Extensions plugin prints out the set of commands that can be used to create macro extensions.  The commands and the instructions for using them are printed to the ImageJ log window.

  • The Stack Slicer plugin is a helper plugin used by the Bio-Formats Importer. It can also be used to split a stack across channels, focal planes or time points.

  • The Bio-Formats Plugins Configuration dialog is a useful way to configure the behavior of the Bio-Formats plugin or each file format. The general tab allows you to configure features of the Bio-Formats plugin such as the display of the slice label (see Bio-Formats plugin configuration options). The Formats tab lists supported file formats and toggles each format on or off, which is useful if your file is detected as the wrong format. It also toggles whether each format bypasses the importer options dialog through the “Windowless” checkbox. You can also configure any specific option for each format (see Additional reader and writer options). The Libraries tab provides a list of available helper libraries used by Bio-Formats.

  • The Bio-Formats Plugins Shortcut Window opens a small window with a quick-launch button for each plugin. Dragging and dropping files onto the shortcut window opens them quickly using the Bio-Formats Importer plugin.

  • The Update Bio-Formats Plugins command will check for updates to the plugins. We recommend you update to the newest Trunk build as soon as you think you may have discovered a bug.