scifio/bioformats

Name: bioformats

Owner: SCIFIO

Description: A fork of the @openmicroscopy/bioformats develop branch, refactored to use @scifio/scifio for image I/O. *EXPERIMENTAL* This project is developed to maintain backwards compatibility, so that Bio-Formats can be converted to the SCIFIO API gradually without breaking any consumers of Bio-Formats.

Created: 2013-06-21 19:58:40.0

Updated: 2014-03-01 23:31:59.0

Pushed: 2013-11-05 20:20:54.0

Homepage: http://scif.io/

Size: 194214

Language: Java

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

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README

Bio-Formats

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.

Purpose

Bio-Formats' primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format. See the statement of purpose for a thorough explanation and rationale.

Supported formats

Bio-Formats supports more than a hundred file formats.

For users

Many software packages use Bio-Formats to read and write microscopy formats.

For developers

You can use Bio-Formats to easily support these formats in your software.

More information

For more information, see the Bio-Formats web site.

Pull request testing

We welcome pull requests from anyone, but ask that you please verify the following before submitting a pull request:

• verify that the branch merges cleanly into `develop`
• verify that the branch compiles with the `clean jars tools` Ant targets
• verify that the branch compiles using Maven
• verify that the branch does not use syntax or API specific to Java 1.6+
• if you are making any build system or packaging changes, verify that OMERO builds when the

• run the unit tests (`ant test`) and correct any failures
• test at least one file in each affected format, using the `showinf` command
• internal developers only: run the data tests. against directories corresponding to the affected format(s), as well as the test_per_commit directory
• make sure that your commits contain the correct authorship information and, if necessary, a signed-off-by line
• make sure that the commit messages or pull request comment contains sufficient information for the reviewer(s) to understand what problem was fixed and how to test it