User Information

Using Bio-Formats with ImageJ and Fiji

The following sections explain the features of Bio-Formats and how to use it within ImageJ and Fiji:

• ImageJ overview
• Fiji overview
• Bio-Formats features in ImageJ and Fiji
• Installing Bio-Formats in ImageJ
• Using Bio-Formats to load images into ImageJ
• Managing memory in ImageJ/Fiji using Bio-Formats
• Bio-Formats plugin configuration options

Command line tools

The Bio-Formats Command line tools (bftools.zip) provide a complete package for carrying out a variety of tasks:

• Command line tools introduction
• Displaying images and metadata
• Converting a file to different format
• Validating XML in an OME-TIFF
• Editing XML in an OME-TIFF
• List formats by domain
• List supported file formats
• Display file in ImageJ
• Format XML data
• Create a high-content screen for testing

OMERO

OMERO 5 uses Bio-Formats to read original files from over 140 file formats. Please refer to the OMERO documentation for further information.

Many other software packages can use Bio-Formats to read and write microscopy formats (click on the package for further details):

Image server applications

• BISQUE
• OME Server

Libraries and scripting applications

• FARSIGHT
• i3dcore
• ImgLib
• ITK
• Qu for MATLAB

Numerical data processing applications

• GNU Octave
• IDL
• KNIME
• MATLAB
• VisAD

Visualization and analysis applications

• Bitplane Imaris
• CellProfiler
• Comstat2
• Endrov
• FocalPoint
• Graphic Converter
• Icy
• Iqm
• Macnification
• Micro-Manager
• MIPAV
• Vaa3D
• VisBio
• XuvTools