# 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

See also

Additional reader and writer 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 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

## 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
- R

## Visualization and analysis applications

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