From cfdfa2e81f753b76d283f9e9762bc91db7a71d26 Mon Sep 17 00:00:00 2001
From: Josh Moore <josh@openmicroscopy.org>
Date: Tue, 29 Aug 2023 11:22:38 +0200
Subject: [PATCH] Update README.md

Fix #60

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

cc: @dgault
---
 README.md | 49 +++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 45 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 17f1935..5bbffab 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,51 @@
-# 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