The OMEZarrReader provides support for reading data following the NGFF specificaiton. It uses the JZarr library from Maven Central for accessing the underlying Zarr data.
The OMEZarrReader has been added to the Bio-Formats development update site (https://sites.imagej.net/Bio-Formats). Be aware that activating it will use a newer version of Bio-Formats.
The jar from this repository can be used in your own code by enabling the OME artifactory repositry:
<repositories>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>central</id>
<name>repo</name>
<url>https://artifacts.openmicroscopy.org/artifactory/repo</url>
</repository>
</repositories>
and adding the dependency:
<dependency>
<groupId>ome</groupId>
<artifactId>OMEZarrReader</artifactId>
<version>${OMEZarrReader.version}</version>
</dependency>
If you would like to use OMEZarrReader with the bftools suite, you will need to set the BC_CP
environment variable to include the jar which includes all dependencies:
BF_CP=target/OMEZarrReader-with-dependencies.jar showinf -nopix your.ome.zarr/.zattrs
- Currently working on packaging, discovered issue when connecting to S3 using packaged jar
- S3 File System Store is likely not ideal sceanrio, other options to be investigated
- S3 access currently very inefficient
- Odd issue with data being lost when decompressing bytes in jzarr, an ugly hack is currently in place
- Identification of S3 location needs updating
- Refactor code to remove duplication
- Parse colours for labels