NGFF-Converter is an open source tool for converting bioimage formats to the OME-TIFF and OME-NGFF 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.
NGFF-Converter releases can be downloaded here:
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 NGFF, then the resulting NGFF 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 is distributed under the terms of the GPL license. Please see LICENSE.txt for further details.
./gradlew clean build
cd build/distributions
unzip *.zip
cd NGFF-Converter-0.1-SNAPSHOT
./bin/NGFF-Converter
NGFF-Converter has the following requirements/dependencies:
- Java 16+
- JavaFX
- bioformats2raw
- raw2ometiff
- blosc
See build.gradle for more precise versioning.
Download prebuilt, signed binaries for these platforms here.
Running from source is possible via the following steps:
Install openjdk-17
sudo apt install openjdk-17-jdk
Install the blosc dependency
sudo apt-get install libblosc-dev
Clone and run the repo