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:

Command line tools

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


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

Libraries and scripting applications

Numerical data processing applications

Visualization and analysis applications