From 2e87ac2b2fe05c0271973dc58404648529b27718 Mon Sep 17 00:00:00 2001 From: David Gault Date: Thu, 14 Dec 2023 15:53:08 +0000 Subject: [PATCH] Update ReadMe to document new reader options --- README.md | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 5bbffab..07c285c 100644 --- a/README.md +++ b/README.md @@ -36,6 +36,10 @@ and adding the 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 +49,13 @@ 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 |