Bio-Formats

Revision as of 12:06, 8 November 2013 by Rueden (talk | contribs) (Update Download links)

OME Bio-Formats plugins (ImageJ)
Author Open Microscopy Environment:
- UW-Madison LOCI
- Glencoe Software
- University of Dundee
Maintainer Curtis Rueden
Melissa Linkert
File See Bio-Formats Downloads page
Source Git
Latest version See Bio-Formats Downloads page
Development status active
Category Category:Import-Export


Purpose

Import data from many life sciences file formats, and export to several open formats.

Documentation

What follows is a brief overview of the available plugins. You will find them all under the "LOCI" submenu of Plugins. See the Bio-Formats web site for additional information about Bio-Formats in general.

See especially the Using Bio-Formats page for detailed instructions.

Bio-Formats Importer

The Bio-Formats Importer is a plugin for reading data into Fiji. It can open many dozens of proprietary life sciences formats, and standardize their acquisition metadata into a common OME data model. It will also extract and set basic metadata values such as spatial calibration if they are available in the file.

Often, you will not need to worry about this plugin to import your data, because Bio-Formats is largely integrated with the File/Open command of Fiji. However, for certain file formats, you may wish to explicitly activate the Bio-Formats Importer to override the default behavior of Fiji. For example, by default Fiji uses some built-in logic to open TIFF files, but this logic may fail with certain TIFFs. The Bio-Formats Importer plugin may be able to import such TIFFs successfully.

Bio-Formats Exporter

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).

Bio-Formats Remote Importer

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 when possible we recommend downloading your data to disk and using the regular Bio-Formats Importer instead.

Bio-Formats Windowless Importer

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

Bio-Formats Macro Extensions

The Bio-Formats plugins come with a set of macro extensions to enable additional functionality from macros. The Bio-Formats Macro Extensions plugin prints out the available commands to the ImageJ log window, along with instructions for using them.

Stack Slicer

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

LOCI Plugins Configuration

The LOCI Plugins Configuration dialog is a useful way to configure the behavior of each file format. You can see a list of supported file formats on the Formats tab, toggle each format on or off (which is useful, for example, if your file is being detected as the wrong format), and toggle whether each format bypasses the importer options dialog using the "Windowless" checkbox. You can also configure any specific options for each format—for example, for QuickTime, you can toggle between Apple's QTJava library or Bio-Formats's built-in support.

In addition, you can see a list of available helper libraries used by Bio-Formats on the Libraries tab.

LOCI Plugins Shortcut Window

The LOCI Plugins Shortcut Window is a small window with a quick-launch button for each LOCI plugin. You can also drag and drop files onto the shortcut window to open them quickly using the Bio-Formats Importer plugin.

Update LOCI Plugins

The Update LOCI Plugins command will check online for updates to the LOCI Plugins. In the case of Fiji, we recommend that you do not use this method of update, but instead use the Fiji Updater.

Scripting

Bio-Formats has a high-level scripting interface, accessible by Java and all scripting languages supported by Fiji (but not the ImageJ macro language). Java example:

String id = "/path/to/myFile.ext";
ImagePlus[] imps = BF.openImagePlus(id);

If needed, import options can be set:

String id = "/path/to/myFile.ext";
ImporterOptions options = new ImporterOptions();
options.setId(id);
options.setAutoscale(true);
options.setCrop(true);
options.setCropRegion(0, new Region(x, y, w, h));
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE);
//...etc.
ImagePlus[] imps = BF.openImagePlus(options);

Daily builds

Fiji ships 4.4.x release versions of Bio-Formats. However, given the long time frame between releases, you can update to the latest code by toggling one of two update sites:

  • Bio-Formats 4 is the latest stable build of version 4.4.x.
  • Bio-Formats 5 is the latest unstable build of version 5.x.

If unsure which to choose, we recommend Bio-Formats 5 because it contains the very latest bugfixes—and when reporting a bug, the developers may ask you to test against Bio-Formats 5 anyway.

To enable the Bio-Formats update site:

  1. Launch the updater: Update Fiji from the Help menu.
  2. Click the Manage update sites button.
  3. Tick the Bio-Formats 5 box:
    Bf-manage-update-sites.png
  4. Click the Close button. The updater should want to update several files now:
    Bf-jars-to-update.png
  5. Click the Apply changes button.
  6. Restart Fiji when prompted.
  7. To verify the upgrade, choose LOCI plugins... from About Plugins beneath the Help menu:
    Bf-about-plugins.png

Source code

The official Bio-Formats 4 source code is at:

   https://github.com/openmicroscopy/bioformats/tree/dev_4_4

The official Bio-Formats 5 source code is at:

   https://github.com/openmicroscopy/bioformats/tree/develop