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.
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.
As of the 4.0.0 release, you can also upgrade the Bio-Formats plugin
directly from ImageJ. Select "Plugins>LOCI>Update LOCI Plugins" from the
ImageJ menu, then select which release you would like to use. You will then
need to restart ImageJ to complete the upgrade process.
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
|
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basicMetadata.txt
|
A macro that uses the Bio-Formats macro extensions to print the
chosen file's basic dimensional parameters to the Log
|
planeTimings.txt
|
A macro that uses the Bio-Formats macro extensions to print the
chosen file's plane timings 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: Wednesday, June 24, 2009
