Update ReadMe and Change Log

CHANGELOG.md

@@ -1,3 +1,27 @@
+0.4.0 (December 2023)
+---------------------
+
+- Updated JZarr dependency to use dev.zarr:jzarr 0.4.0 [#54](https://github.com/ome/ZarrReader/pull/54)
+- Removed duplicate declaration from POM file [#56](https://github.com/ome/ZarrReader/pull/56)
+- Use canonical path for calls to ZarrService [#57](https://github.com/ome/ZarrReader/pull/57)
+- Updated GitHub actions checkout to V3 [#59](https://github.com/ome/ZarrReader/pull/59)
+- Updated ReadMe installation instructions and requirements [#62](https://github.com/ome/ZarrReader/pull/62)
+- Implemented performance improvements and introduced new reader options [#64](https://github.com/ome/ZarrReader/pull/64)
+- Bumped the Bio-Formats version to 7.0.0 [#65](https://github.com/ome/ZarrReader/pull/65)
+- Bumped dev.zarr:jzarr to 0.4.2 [#66](https://github.com/ome/ZarrReader/pull/66)
+
+0.3.1 (March 2023)
+------------------
+
+- Updated GitHub Actions output commands [#42](https://github.com/ome/ZarrReader/pull/42)
+- Upgraded GitHub Actions setup-java action [#47](https://github.com/ome/ZarrReader/pull/47)
+- Fixed handling of pre-existing plate metadata to avoid duplicate keys [#49](https://github.com/ome/ZarrReader/pull/49)
+
+0.3.0 (June 2022)
+-----------------
+
+- Updated a number of dependencies [#38](https://github.com/ome/ZarrReader/pull/38)
+
 0.2.0 (May 2022)
 ------------------
 

README.md

@@ -36,6 +36,10 @@ and adding the dependency:
 </dependency>
 ```
 
+### Releases
+
+Release versions of OMEZarrReader are also available directly from the [OME artifactory](https://artifacts.openmicroscopy.org/artifactory/webapp/browserepo.html?0&pathId=ome.releases:ome/OMEZarrReader)
+
 ### Bio-Formats tools
 
 If you would like to use OMEZarrReader with the bftools suite, you will need to set the `BC_CP`
@@ -45,11 +49,15 @@ 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
-- 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
+## Reader specific options
+
+The OMEZarrReader has a number of reader specific options which can be used to customise the reader behaviour. This options can be used in the same manner as the reader options for Bio-Formats outlined [here](https://bio-formats.readthedocs.io/en/latest/formats/options.html#usage). 
+
+The list of available options are below:
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `omezarr.quick_read` | false | Improves the read performance by limiting the number of files that are parsed. This assumes that the shape and resolution count of all images in a plate remains constant  |
+| `omezarr.save_annotations` | false | Determines if all the Zarr JSON metadata should be stored as XML annotations in the OME Model |
+| `omezarr.list_pixels` | false | Used to decide if getUsedFiles should list all of the pixel chunks |
+| `omezarr.include_labels` | false | Used to decide if images stored in the label sub folder should be included in the list of images |