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.
Installation
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.
Usage
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.
For a more detailed description of each plugin, see the Bio-Formats page of the Fiji wiki.
Upgrading
To upgrade, just overwrite the old loci_tools.jar with the latest one.
Step-by-step upgrade instructions for Windows are available here.
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.
Macros and Plugins
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 |
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 |
batchTiffConvert.txt |
This macro converts all files in a directory to TIFF using the Bio-Formats macro extensions. |
Simple_Read |
A very simple plugin that demonstrates the easiest way to use Bio-Formats to read files. |
Read_Image |
A plugin that demonstrates how to use Bio-Formats to read data into ImageJ one slice at a time. This is a lower level approach than the Simple_Read plugin. |
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 |