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Fix ome#60

- [x] remove previous custom jar requirements
- [x] add current installation instructions
- [ ] review TODOs

cc: @dgault
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joshmoore authored Aug 29, 2023
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# ZarrReader
# OMEZarrReader

Requires custom jzarr: https://github.com/dgault/jzarr/tree/ome-zarr
The OMEZarrReader provides support for reading data following the [NGFF](https://ngff.openmicroscopy.org/)
specificaiton. It uses the [JZarr](https://github.com/zarr-developers/jzarr) library from [Maven Central](https://central.sonatype.com/artifact/dev.zarr/jzarr/) for accessing the underlying Zarr data.

Requires Bio-Formats update to add reader: https://github.com/ome/bioformats/pull/3639
## Installation

Known Issues/TODO list:
### Fiji Update Site

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.

### Maven

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>
```

### Bio-Formats tools

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
```

## Known Issues/TODO list
- 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
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