OME at LOCI –
Software – Bio-Formats — ImageJ
ImageJ is an image processing
and analysis application written in Java, widely used in the life
sciences fields, with an extensible plugin infrastructure.
You can use Bio-Formats as a plugin for ImageJ to read and write
images in the formats it supports.
Download loci-tools.jar and
drop it into your ImageJ/plugins folder. Next time you run ImageJ,
a new LOCI submenu with several plugins will appear in the Plugins menu,
including the Bio-Formats Importer and Bio-Formats Exporter.
If you wish to read certain kinds of compressed DICOM files, you will
need to
set up the optional native libraries.
The Bio-Formats Importer plugin can display image stacks in several ways:
- In a standard ImageJ window (including as a hyperstack)
- Using our Data Browser plugin
(included)
- With Joachim Walter's
Image5D
plugin (if installed)
- With Rainer Heintzmann's
View5D plugin
(if installed)
ImageJ v1.37 and later automatically (via HandleExtraFileTypes) calls the
Bio-Formats logic, if installed, as needed when a file is opened within
ImageJ—e.g., when using File/Open instead of explicitly choosing
"Bio-Formats Importer" from the Plugins/LOCI menu.
To upgrade, just overwrite the old loci_tools.jar with the
latest one.
You may want to download the latest version of ImageJ first,
to take advantage of new features and bugfixes.
Bio-Formats is fully scriptable in a macro, and callable from a plugin.
To use in a macro, use the Macro Recorder to record a call to the
Bio-Formats Importer with the desired options. You can also perform
more targeted metadata queries using the Bio-Formats macro extensions.
Here are some example macros and plugins to get you started:
|
Sample ImageJ macros and plugins that use Bio-Formats
|
|---|
basicMetadata.txt
|
A macro that uses the Bio-Formats macro extensions to print the
chosen file's basic dimensional parameters to the Log
|
recursiveTiffConvert.txt
|
A macro for recursively converting files to TIFF using Bio-Formats
|
bfOpenAsHyperstack.txt
|
This macro from Wayne Rasband opens a file as a hyperstack using
only the Bio-Formats macro extensions (without calling the
Bio-Formats Importer plugin)
|
zvi2HyperStack.txt
|
This macro from Sebastien Huart reads in a ZVI file using
Bio-Formats, synthesizes the LUT using emission wavelength
metadata, and displays the result as a hyperstack
|
dvSplitTimePoints.txt
|
This macro from Sebastien Huart splits timepoints/channels
on all DV files in a folder
|
Read_Image
|
A simple plugin that demonstrates how to use Bio-Formats to
read files into ImageJ
|
Mass_Importer
|
A simple plugin 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
|
Last update: Friday, July 11, 2008
