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Using Bio-Formats as a Java library

Bio-Formats as a Maven, Gradle or Ivy dependency

All released .jar artifacts are published to and can be obtained from the OME Artifactory. The “Client Settings” section of the Artifactory main page provides example code snippets for inclusion into your Gradle, Maven or Ivy project, which will enable the use of this repository.

Examples of getting started with Bio-Formats using Maven or Gradle are given in the repository. OMERO uses Ivy to manage its Java dependencies including Bio-Formats.


In order to retrieve the NetCDF dependency of Bio-Formats, it is necessary to configure the Unidata releases repository in addition to Maven Central and the OME artifactory in your pom.xml, build.gradle or ivy.xml file.

Bio-Formats as a Java library

Alternatively Bio-Formats can be used by including its component jar files. You can download formats-gpl.jar to use it as a library. Just add formats-gpl.jar to your CLASSPATH or build path. You will also need ome-common.jar for common I/O functions, ome-xml.jar for metadata standardization, and SLF4J for Logging.


The complete list of current dependencies is as follows:

Package Maven name License
Logback Classic v1.1.1 ch.qos.logback:logback-classic:1.1.1 Eclipse Public License v1.0
Logback Core v1.1.1 ch.qos.logback:logback-core:1.1.1 Eclipse Public License v1.0
JHDF5 v14.12.0 Apache License v2.0
XMP Library for Java v5.1.2 com.adobe.xmp:xmpcore:5.1.2 BSD License
JCommander v1.27 com.beust:jcommander:1.27 Apache License v2.0
metadata-extractor v2.6.2 com.drewnoakes:metadata-extractor:2.6.2 Apache License v2.0
Kryo v2.24.0 com.esotericsoftware.kryo:kryo:2.24.0 BSD License
MinLog v1.2 com.esotericsoftware.minlog:minlog:1.2 BSD License
Guava v17.0 Apache License v2.0
JGoodies Common v1.7.0 com.jgoodies:jgoodies-common:1.7.0 BSD License
JGoodies Forms v1.7.2 com.jgoodies:jgoodies-forms:1.7.2 BSD License
Commons Collections v3.2.1 commons-collections:commons-collections:3.2.1 Apache License v2.0
Commons Lang v2.4 commons-lang:commons-lang:2.4 Apache License v2.0
Commons Logging v1.1.1 commons-logging:commons-logging:1.1.1 Apache License v2.0
NetCDF-Java Library v4.3.22 edu.ucar:netcdf:4.3.22 MIT-Style License
Joda time v2.2 joda-time:joda-time:2.2 Apache License v2.0
JUnit v4.10 junit:junit:4.10 Common Public License v1.0
Apache Log4j v1.2.17 log4j:log4j:1.2.17 Apache License v2.0
ImageJ v1.48s net.imagej:ij:1.48s Public domain
Assume NG v1.2.4 nl.javadude.assumeng:assumeng:1.2.4 Apache License v2.0
Apache Velocity v1.6.4 org.apache.velocity:velocity:1.6.4 Apache License v2.0
BeanShell v2.0b4 org.beanshell:bsh:2.0b4 Sun Public License / LGPL
Hamcrest Core v1.1 org.hamcrest:hamcrest-core:1.1 BSD 3-Clause
Objenesis v2.1 org.objenesis:objenesis:2.1 Apache License v2.0
Perf4J v0.9.13 org.perf4j:perf4j:0.9.13 Apache License v2.0
Native Library Loader v2.1.4 org.scijava:native-lib-loader:2.1.4 BSD License
SLF4J API v1.7.4 org.slf4j:slf4j-api:1.7.6 MIT License
SLF4J LOG4J-12 Binding v1.7.6 org.slf4j:slf4j-log4j12:1.7.6 MIT License
TestNG v6.8 org.testng:testng:6.8 Apache License v2.0
SnakeYAML v1.6 org.yaml:snakeyaml:1.6 Apache License v2.0
Jakarta ORO v2.0.8 oro:oro:2.0.8 Apache License v2.0
Woolz v1.4.0 woolz:JWlz:1.4.0 GPL v2
Xalan Java Serializer v2.7.2 xalan:serializer:2.7.2 Apache License v2.0
Xalan Java v2.7.2 xalan:xalan:2.7.2 Apache License v2.0
Xerces2 Java Parser v2.8.1 xerces:xercesImpl:2.8.1 Apache License v2.0
XML Commons External Components XML APIs v1.3.04 xml-apis:xml-apis:1.3.04 Apache License v2.0

As described in Versioning policy, the minor version number of a Bio-Formats release will always be increased if the version of a non-OME/external dependency is bumped.

Examples of usage

File reading and performance:

MultiFileExample - Simple example of how to open multiple files simultaneously.

ParallelRead - Reads all files in given directory in parallel, using a separate thread for each.

ReadWriteInMemory - Tests the Bio-Formats I/O logic to and from byte arrays in memory.

File writing:

MinimumWriter - A command line utility demonstrating the minimum amount of metadata needed to write a file.

TiledExport - Shows how to convert a file one tile at a time, instead of one plane at a time (needed for very large images).

File compression:

makeLZW - Converts the given image file to an LZW-compressed TIFF.

Metadata extract/print:

GetPhysicalMetadata - Uses Bio-Formats to extract some basic standardized (format-independent) metadata.

ImageInfo - A more involved command line utility for thoroughly reading an input file, printing some information about it, and displaying the pixels onscreen using the Bio-Formats viewer.

PrintTimestamps - A command line example demonstrating how to extract timestamps from a file.

PrintLensNA - Uses Bio-Formats to extract lens numerical aperture in a format-independent manner from a dataset.

PrintROIs - A simple example of how to retrieve ROI data parsed from a file.

SubResolutionExample - Demonstration of the sub-resolution API.

Metadata add/edit:

EditImageName - Edits the given file’s image name (but does not save back to disk).

EditTiffComment - Allows raw user TIFF comment editing for the given TIFF files.

writeMapAnnotations - Example method to write MapAnnotations to the ome-xml.

CommentSurgery - Edits a TIFF ImageDescription comment, particularly the OME-XML comment found in OME-TIFF files.

Image converters:

ImageConverter - A simple command line tool for converting between formats.

ConvertToOmeTiff - Converts the given files to OME-TIFF format.

WritePreCompressedPlanes - Writes the pixels from a set of JPEG files to a single TIFF. The pixel data is used as-is, so no decompression or re-compression is performed.

ImageJ plugins:

Simple_Read - A simple ImageJ plugin demonstrating how to use Bio-Formats to read files into ImageJ (see ImageJ overview).

Read_Image - An ImageJ plugin that uses Bio-Formats to build up an image stack, reading image planes one by one (see ImageJ overview).

Mass_Importer - A simple plugin for ImageJ that demonstrates how to open all image files in a directory using Bio-Formats, grouping files with similar names to avoiding opening the same dataset more than once (see ImageJ overview).

Image processing utilities:

SewTiffs - Stitches the first plane from a collection of TIFFs into a single file.

SumPlanes - Sums together the image planes from the given file,and saves the result to a 16-bit TIFF.

A Note on Java Web Start (bioformats_package.jar vs. formats-gpl.jar)

To use Bio-Formats with your Java Web Start application, we recommend using formats-gpl.jar rather than bioformats_package.jar—the latter is merely a bundle of formats-gpl.jar plus all its optional dependencies.

The bioformats_package.jar bundle is intended as a convenience (e.g. to simplify installation as an ImageJ plugin), but is by no means the only solution for developers. We recommend using formats-gpl.jar as a separate entity depending on your needs as a developer.

The bundle is quite large because we have added support for several formats that need large helper libraries (e.g. Imaris’ HDF-based format). However, these additional libraries are optional; Bio-Formats has been coded using reflection so that it can both compile and run without them.

When deploying a JNLP-based application, using bioformats_package.jar directly is not the best approach, since every time Bio-Formats is updated, the server would need to feed another 15+ MB JAR file to the client. Rather, Web Start is a case where you should keep the JARs separate, since JNLP was designed to make management of JAR dependencies trivial for the end user. By keeping formats-gpl.jar and the optional dependencies separate, only a <1 MB JAR needs to be updated when formats-gpl.jar changes.

As a developer, you have the option of packaging formats-gpl.jar with as many or as few optional libraries as you wish, to cut down on file size as needed. You are free to make whatever kind of “stripped down” version you require. You could even build a custom formats-gpl.jar that excludes certain classes, if you like.