# User Information

Every release of Bio-Formats includes a plugin for ImageJ/Fiji, a set of command line utilities and a MATLAB toolbox.

## 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

See also

Additional reader and writer options

## Command line tools

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

- Command line tools overview
- 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
- “Precompressed” tiles

See also

Additional reader and writer options

## Using Bio-Formats in MATLAB/Octave

The following pages explain how to install and use Bio-Formats in MATLAB or Octave:

- MATLAB
- GNU Octave

## Third-party applications

Several third-party libraries and applications use Bio-Formats to read and write imaging formats. All the examples below are maintained outside the Bio-Formats development release cycle. Any usage question should be raised with their respective development team.

### OMERO

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

### 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
- R

### Visualization and analysis applications

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