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 bioformats_package.jar and drop it into your ImageJ/plugins folder. Next time you run ImageJ, a new Bio-Formats 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:
ImageJ v1.37 and later automatically (via HandleExtraFileTypes) calls the Bio-Formats logic, if installed, as needed when a file is opened within ImageJ, i.e. when using File ‣ Open instead of explicitly choosing Plugins ‣ Bio-Formats ‣ Bio-Formats Importer from the menu.
For a more detailed description of each plugin, see the Bio-Formats page of the ImageJ wiki.
To upgrade, just overwrite the old bioformats_package.jar with the latest one.
You can also upgrade the Bio-Formats plugin directly from ImageJ. Select Plugins ‣ Bio-Formats ‣ Update Bio-Formats 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 ImageJ macros and plugins that use Bio-Formats to get you started:
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.
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.