NGFF-Converter is an open source tool for converting bioimage formats to the OME-TIFF and OME-Zarr specifications.
Formats supported by the Bio-Formats library should be able to be converted by this tool. Internally NGFF-Converter uses the bioformats2raw and raw2ometiff packages for conversion. With default settings, the resulting files should automatically have resolution pyramids generated if needed.
Release notes detailing changes between versions can be found here
NGFF-Converter is not supported on Linux. To convert files on Linux, please use the bioformats2raw and raw2ometiff command line tools.
Pre-built signed Windows and MacOS artifacts can be downloaded for the latest NGFF-Converter release here:
- The underlying bioformats package is currently unable to read some formats on ARM-based MacOS systems.
Running the tool will display a desktop GUI:
Files can be dragged and dropped onto this window to add them as conversion jobs. By default you'll see a window requesting some basic settings when adding jobs.
When conversion jobs are added, you'll see a different interface with two lists. Each conversion "Job" is divided into multiple "Tasks" within each job. For example, converting .png to .ome.tiff requires two steps: The PNG is converted to OME-Zarr, then the resulting OME-Zarr file is converted to TIFF. A third "Output" job offers settings for where to save the final result.
Clicking on the 'Configure' (cog) icon allows you to edit the settings for a specific job. Each task within a job has it's own configuration options.
For example, configuring the "Output" task will allow you to change the destination directory or filename.
From the main window, jobs can be started using the "Run" buttons. Only a single job will execute at a given time, any others will be queued. Job progress will be displayed next to the individual tasks. If all goes well, the job's status will change to "completed".
If anything goes wrong a "Failed" status will display. Each job has it's own individual execution logs which may provide detail on what prevented the conversion. Hovering over the status label will also attempt to display any error messages. Please note that it is possible to configure settings of individual tasks in ways which are incompatible with later workflow steps. The "help" icon next to each setting provides warnings about particularly disruptive settings.
If you need further help, please feel free to raise an issue.
NGFF-Converter has the following requirements/dependencies:
- Java 17+
- JavaFX
- bioformats2raw
- raw2ometiff
See build.gradle for more precise versioning.
Clone the repository:
git clone https://github.com/glencoesoftware/NGFF-Converter
Run the build command:
./gradlew clean build
cd build/distributions
unzip *.zip
cd NGFF-Converter-0.1-SNAPSHOT
./bin/NGFF-Converter
NGFF-Converter is distributed under the terms of the GPL license. Please see LICENSE.txt for further details.