A Docker image based on openmicroscopy/omero-web with an already installed ome_seadragon plugin.
A running openmicroscopy/omero-server.
It is strongly encouraged the usage of the crs4/ome_seadragon-nginx Docker image as web server.
The server can be configured using the following environment variables:
OMEROHOST the OMERO server hosting the data
OMEROPORT (default 4064) the port of the OMERO server
ROOTPASS (default omero) root password for OMERO server
IMAGES_REPOSITORY (default /OMERO/)
OME_SEADRAGON_COOKIE (default ome_seadragon_web) the cookie used by OMERO web server
For more details on OMERO web configuration, please refere to the official documentation
IMAGES_FOLDER (default None) the folder containing the images managed by OMERO server, only needed if different than default one which is $IMAGES_REPOSITORY/ManagedRepository/
OME_PUBLIC_GROUP (default ome_public_data) the default group for OMERO public user
OME_PUBLIC_USER_NAME (default ome_public) OMERO default public user
OME_PUBLIC_USER_PASS (default omero) OMERO public user's default password
OME_PUBLIC_URL_FILTER (default ^/ome_seadragon) the default URL filter used in combination with OMERO public user, for further details please check OMERO server documentation
DEFAULT_OME_GROUP (default None) if OMERO public user belongs to more than one group, this is the default group to search for images, projects, datasets and tags
REDISHOST (default None) Redis host that will be used as cache server. If not specified, cache won't be enabled.
REDISPORT (default 6379) Redis server's port
REDISDB (default 0) Redis server's database ID
CACHE_EXPIRE_TIME (default '{"hours": 8}') the expire time for tiles and thumbnails stored in cache. This value is expressed as a JSON string and one or a combination of the following keys are accepted days hours minutes and seconds
GW_USER_NAME (default None) OMERO user used to login if an ome_seadragon_gateway server is enabled
GW_USER_PASS (default None) password for GW_USER_NAME user
GW_USER_GROUP (default ome_gw_data) the default group for the GW_USER_NAME user. If it doen't exits, it will be automatically created.
Important: if GW_USER_NAME user doesn't exist in the system but both GW_USER_NAME and GW_USER_PASS are provided, it will be automatically created and associated to GW_USER_GROUP group
Important: only two rendering engines are supported at the moment openslide and omero. If different values are specified, this will result in an error.
TILES_PRIMARY_ENGINE (default openslide) the primary tiles rendering engine. If openslide is used as primary, omero will be used as secondary engine and vice versa
THUMBNAILS_PRIMARY_ENGINE (default openslide) the primary thumbnails rendering engine. If openslide is used as primary, omero will be used as secondary engine and vice versa
TILES_OVERLAP (default 1) specify how many pixels each tile will overlap with the next ones
TILES_FORMAT (default jpeg) the file of the tiles. It can be jpeg or png
JPEG_TILES_QUALITY (default 90) the quality of JPEG compressed tiles. Only applied if jpeg is set for TILES_FORMAT variable
SLIDE_LIMIT_BOUNDS (default True) if True, only render only the non-empty slide region. This only applies when rendering slides using openslide engine (regardless of whether it's primary or secondary)
TILES_SIZE (default 256) the size in pixels of a tile's border. Tiles are always retrieved as squares
DATASETS_REPOSITORY (default /data/array_datasets/) the folder containing the datasets managed as heatmaps by ome_seadragon
A Docker compose example to run a complete ome_seadragon stack can be found here