Index

Symbols

--advanced-help omero-import command line option --all omero-help command line option --archived omero-fs-images command line option --check omero-fs-sets command line option --debug DEBUG omero-import command line option --depth DEPTH omero-import command line option --dry-run omero-chgrp command line option omero-chown command line option omero-delete command line option --email EMAIL omero-import command line option --exclude omero-chgrp command line option omero-chown command line option omero-delete command line option --extended omero-fs-images command line option omero-fs-sets command line option --force omero-delete command line option --force-rewrite omero-admin-start command line option omero-admin-stop command line option --foreground omero-admin-start command line option --groups omero-fs-usage command line option --include omero-chgrp command line option omero-chown command line option omero-delete command line option --iterate Dataset:<id> omero-export command line option --java-help omero-import command line option --limit LIMIT omero-fs-images command line option omero-fs-sets command line option --list omero-help command line option --logs omero-import command line option --managed omero-fs-repos command line option --markers setup.py-test command line option --no-move omero-fs-rename command line option --offset OFFSET omero-fs-images command line option omero-fs-sets command line option --order {newest,oldest,prefix} omero-fs-images command line option omero-fs-sets command line option --ordered omero-chgrp command line option omero-chown command line option omero-delete command line option --parents omero-fs-mkdir command line option --recursive omero-help command line option --repeat <number> py.test command line option --report omero-chgrp command line option omero-chown command line option omero-delete command line option omero-fs-usage command line option omero-import command line option --size_only omero-fs-usage command line option --skip SKIP omero-import command line option --style {plain,csv,json,sql} omero-fs-images command line option omero-fs-repos command line option omero-fs-sets command line option omero-fs-usage command line option

--sudo ADMINUSER|GROUPOWNER omero-login command line option --units {K,M,G,T,P} omero-fs-usage command line option --upload omero-import command line option --wait WAIT omero-fs-usage command line option --with-transfer WITH_TRANSFER [WITH_TRANSFER ...] omero-fs-sets command line option --without-images omero-fs-sets command line option -d DATASET_ID, -T TARGET, --target TARGET omero-import command line option -DCMAKE_CXX_FLAGS cmake command line option -DCMAKE_EXE_LINKER_FLAGS cmake command line option -DCMAKE_INCLUDE_PATH cmake command line option -DCMAKE_LIBRARY_PATH cmake command line option -DCMAKE_MODULE_LINKER_FLAGS cmake command line option -DCMAKE_PREFIX_PATH cmake command line option -DCMAKE_PROGRAM_PATH cmake command line option -DCMAKE_SHARED_LINKER_FLAGS cmake command line option -DCMAKE_VERBOSE_MAKEFILE cmake command line option -DIce_<C>_LIBRARIES cmake command line option -DIce_DEBUG cmake command line option -DIce_HOME cmake command line option -DIce_INCLUDE_DIR cmake command line option -DIce_SLICE2XXX_EXECUTABLE cmake command line option -DIce_SLICE_DIR cmake command line option -f omero-import command line option -g GROUP, --group GROUP omero-login command line option -h, --help omero-admin-start command line option omero-admin-stop command line option omero-fs-images command line option omero-fs-mkdir command line option omero-fs-rename command line option omero-fs-repos command line option omero-fs-sets command line option omero-fs-usage command line option omero-import command line option py.test command line option setup.py-test command line option -k <string> setup.py-test command line option -k KEY, --key KEY omero-login command line option -m <marker> setup.py-test command line option -p PORT, --port PORT omero-login command line option -s setup.py-test command line option -s SERVER, --server SERVER omero-login command line option -s SERVER, -p PORT, -U USERNAME, -g GROUPNAME omero-import command line option -t <test_path>, --test-path <test_path> setup.py-test command line option -u USER, --user USER omero-login command line option -w PASSWORD, --password PASSWORD omero-login command line option

A

Action Add Users to Groups addData() (omero.grid.Table method) Administrator

AgentEvent AgentEventListener Analyst Annotate

B

broken

C

ch.qos.logback.core.Appender.error Change ownership Chgrp Chown cmake command line option -DCMAKE_CXX_FLAGS -DCMAKE_EXE_LINKER_FLAGS -DCMAKE_INCLUDE_PATH -DCMAKE_LIBRARY_PATH -DCMAKE_MODULE_LINKER_FLAGS -DCMAKE_PREFIX_PATH -DCMAKE_PROGRAM_PATH -DCMAKE_SHARED_LINKER_FLAGS -DCMAKE_VERBOSE_MAKEFILE -DIce_<C>_LIBRARIES -DIce_DEBUG -DIce_HOME -DIce_INCLUDE_DIR -DIce_SLICE2XXX_EXECUTABLE -DIce_SLICE_DIR

CMAKE_INCLUDE_PATH, [1] CMAKE_LIBRARY_PATH columns (omero.grid.Data attribute) CompletionHandler connection omero-login command line option Create and Edit Groups Create and Edit Users CXX CXXFLAGS, [1]

D

Data Viewer Delete

Delete Data DYLD_LIBRARY_PATH, [1]

E

Edit environment variable CMAKE_INCLUDE_PATH, [1] CMAKE_LIBRARY_PATH CXX CXXFLAGS, [1] DYLD_LIBRARY_PATH, [1] GTEST_ROOT ICE_CONFIG, [1], [2], [3], [4], [5], [6] ICE_HOME, [1] JAVA_OPTS, [1] LD_LIBRARY_PATH, [1] OMERO_CONFIG OMERO_HOME, [1], [2], [3], [4], [5], [6] OMERO_PREFIX, [1], [2], [3], [4] OMERO_SERVER OMERO_SESSIONDIR, [1], [2], [3], [4] OMERO_SESSION_DIR, [1], [2] OMERO_TMPDIR, [1], [2], [3] OMERO_USERDIR, [1], [2] PATH, [1], [2], [3], [4] PYTHONPATH, [1], [2], [3], [4], [5], [6], [7], [8], [9] SLICEPATH, [1] VERBOSE

EventBus EventBusListener

G

getAllMetadata() (omero.grid.Table method) getHeaders() (omero.grid.Table method) getMetadata() (omero.grid.Table method) getNumberOfRows() (omero.grid.Table method)

getWhereList() (omero.grid.Table method) Group and Data Organizer Group member Group owner GTEST_ROOT

I

Ice.IPv6 ICE_CONFIG, [1], [2], [3], [4], [5], [6]

ICE_HOME, [1] Importer initialize() (omero.grid.Table method)

J

JAVA_OPTS, [1]

jvm.fileDescriptorCountRatio

L

lastModification (omero.grid.Data attribute)

LD_LIBRARY_PATH, [1]

M

ManualStrategy

Mix data Move between groups

O

ome.io.nio.PixelsService.minmaxTimes ome.io.nio.PixelsService.tileTimes` ome.services.eventlogs.EventLogQueue.priorityCount omero-admin-start command line option --force-rewrite --foreground -h, --help omero-admin-stop command line option --force-rewrite -h, --help omero-chgrp command line option --dry-run --exclude --include --ordered --report omero-chown command line option --dry-run --exclude --include --ordered --report omero-delete command line option --dry-run --exclude --force --include --ordered --report omero-export command line option --iterate Dataset:<id> omero-fs-images command line option --archived --extended --limit LIMIT --offset OFFSET --order {newest,oldest,prefix} --style {plain,csv,json,sql} -h, --help omero-fs-mkdir command line option --parents -h, --help omero-fs-rename command line option --no-move -h, --help omero-fs-repos command line option --managed --style {plain,csv,json,sql} -h, --help omero-fs-sets command line option --check --extended --limit LIMIT --offset OFFSET --order {newest,oldest,prefix} --style {plain,csv,json,sql} --with-transfer WITH_TRANSFER [WITH_TRANSFER ...] --without-images -h, --help omero-fs-usage command line option --groups --report --size_only --style {plain,csv,json,sql} --units {K,M,G,T,P} --wait WAIT -h, --help omero-help command line option --all --list --recursive omero-import command line option --advanced-help --debug DEBUG --depth DEPTH --email EMAIL --java-help --logs --report --skip SKIP --upload -d DATASET_ID, -T TARGET, --target TARGET -f -h, --help -s SERVER, -p PORT, -U USERNAME, -g GROUPNAME omero-login command line option --sudo ADMINUSER|GROUPOWNER -g GROUP, --group GROUP -k KEY, --key KEY -p PORT, --port PORT -s SERVER, --server SERVER -u USER, --user USER -w PASSWORD, --password PASSWORD connection omero.checksum.supported omero.client.browser.thumb_default_size omero.client.download_as.max_size omero.client.scripts_to_ignore omero.client.ui.menu.dropdown.colleagues.enabled omero.client.ui.menu.dropdown.colleagues.label omero.client.ui.menu.dropdown.everyone.enabled omero.client.ui.menu.dropdown.everyone.label omero.client.ui.menu.dropdown.leaders.enabled omero.client.ui.menu.dropdown.leaders.label omero.client.ui.tree.orphans.description omero.client.ui.tree.orphans.enabled omero.client.ui.tree.orphans.name omero.client.ui.tree.type_order omero.client.viewer.initial_zoom_level omero.client.viewer.interpolate_pixels omero.client.viewer.roi_limit omero.client.web.host omero.cluster.read_only omero.cluster.redirector omero.data.dir omero.db.authority omero.db.dialect omero.db.driver omero.db.host omero.db.name omero.db.pass omero.db.patch omero.db.poolsize omero.db.port omero.db.prepared_statement_cache_size omero.db.profile omero.db.sql_action_class omero.db.statistics omero.db.user omero.db.version omero.fs.repo.path omero.fs.repo.path_rules omero.grid.BoolColumn (built-in class) omero.grid.Column (built-in class) omero.grid.Data (built-in class) omero.grid.DoubleArrayColumn (built-in class) omero.grid.DoubleColumn (built-in class) omero.grid.FileColumn (built-in class) omero.grid.FloatArrayColumn (built-in class) omero.grid.ImageColumn (built-in class) omero.grid.LongArrayColumn (built-in class) omero.grid.LongColumn (built-in class) omero.grid.PlateColumn (built-in class) omero.grid.registry_timeout omero.grid.RoiColumn (built-in class) omero.grid.StringColumn (built-in class) omero.grid.Table (built-in class) omero.grid.Tables (built-in class) omero.grid.WellColumn (built-in class) omero.jvmcfg.append omero.jvmcfg.heap_dump omero.jvmcfg.heap_size omero.jvmcfg.max_system_memory omero.jvmcfg.min_system_memory omero.jvmcfg.percent omero.jvmcfg.perm_gen omero.jvmcfg.strategy omero.jvmcfg.system_memory omero.launcher.jython omero.launcher.matlab omero.launcher.python omero.ldap.base omero.ldap.config omero.ldap.group_filter

omero.ldap.group_mapping omero.ldap.new_user_group omero.ldap.new_user_group_owner omero.ldap.password omero.ldap.referral omero.ldap.sync_on_login omero.ldap.urls omero.ldap.user_filter omero.ldap.user_mapping omero.ldap.username omero.mail.bean omero.mail.config omero.mail.from omero.mail.host omero.mail.password omero.mail.port omero.mail.smtp.auth omero.mail.smtp.connectiontimeout omero.mail.smtp.debug omero.mail.smtp.socketFactory.class omero.mail.smtp.socketFactory.fallback omero.mail.smtp.socketFactory.port omero.mail.smtp.starttls.enable omero.mail.smtp.timeout omero.mail.transport.protocol omero.mail.username omero.managed.dir omero.metrics.bean omero.metrics.graphite omero.metrics.slf4j_minutes omero.pixeldata.backoff omero.pixeldata.backoff.default omero.pixeldata.backoff.maxpixels omero.pixeldata.batch omero.pixeldata.cron omero.pixeldata.dispose omero.pixeldata.event_log_loader omero.pixeldata.max_plane_height omero.pixeldata.max_plane_width omero.pixeldata.memoizer_wait omero.pixeldata.repetitions omero.pixeldata.threads omero.pixeldata.tile_height omero.pixeldata.tile_sizes_bean omero.pixeldata.tile_width omero.policy.bean omero.policy.binary_access omero.ports.prefix omero.ports.registry omero.ports.ssl omero.ports.tcp omero.process.jython omero.process.matlab omero.process.python omero.scripts.cache.cron omero.scripts.cache.spec omero.scripts.timeout omero.search.analyzer omero.search.batch omero.search.bridges omero.search.cron omero.search.event_log_loader omero.search.excludes omero.search.include_actions omero.search.include_types omero.search.locking_strategy omero.search.max_file_size omero.search.max_partition_size omero.search.maxclause omero.search.merge_factor omero.search.ram_buffer_size omero.search.repetitions omero.search.reporting_loops omero.security.chmod_strategy omero.security.filter.bitand omero.security.keyStore omero.security.keyStorePassword omero.security.login_failure_throttle_count omero.security.login_failure_throttle_time omero.security.password_provider omero.security.password_required omero.security.trustStore omero.security.trustStorePassword omero.sessions.maximum omero.sessions.sync_force omero.sessions.sync_interval omero.sessions.timeout omero.threads.cancel_timeout omero.threads.idle_timeout omero.threads.max_threads omero.threads.min_threads omero.throttling.method_time.error omero.throttling.method_time.error.indexer omero.throttling.method_time.warn omero.throttling.method_time.warn.indexer omero.throttling.objects_read_interval omero.throttling.objects_written_interval omero.throttling.servants_per_session omero.web.admins omero.web.application_server omero.web.application_server.host omero.web.application_server.max_requests omero.web.application_server.port omero.web.apps omero.web.base_include_template omero.web.caches omero.web.chunk_size omero.web.cors_origin_allow_all omero.web.cors_origin_whitelist omero.web.databases omero.web.debug omero.web.index_template omero.web.logdir omero.web.login_logo omero.web.login_redirect omero.web.login_view omero.web.middleware omero.web.open_with omero.web.page_size omero.web.ping_interval omero.web.pipeline_css_compressor omero.web.pipeline_js_compressor omero.web.pipeline_staticfile_storage omero.web.prefix omero.web.public.cache.enabled omero.web.public.cache.key omero.web.public.cache.timeout omero.web.public.enabled omero.web.public.get_only omero.web.public.password omero.web.public.server_id omero.web.public.url_filter omero.web.public.user omero.web.secret_key omero.web.secure omero.web.secure_proxy_ssl_header omero.web.server_list omero.web.session_cookie_age omero.web.session_cookie_domain omero.web.session_cookie_name omero.web.session_engine omero.web.session_expire_at_browser_close omero.web.static_root omero.web.static_url omero.web.staticfile_dirs omero.web.template_dirs omero.web.thumbnails_batch omero.web.ui.center_plugins omero.web.ui.metadata_panes omero.web.ui.right_plugins omero.web.ui.top_links omero.web.use_x_forwarded_host omero.web.viewer.view omero.web.webgateway_cache omero.web.wsgi_args omero.web.wsgi_timeout omero.web.wsgi_workers OMERO_CONFIG OMERO_HOME, [1], [2], [3], [4], [5], [6] OMERO_PREFIX, [1], [2], [3], [4] OMERO_SERVER OMERO_SESSION_DIR, [1], [2] OMERO_SESSIONDIR, [1], [2], [3], [4] OMERO_TMPDIR, [1], [2], [3] OMERO_USERDIR, [1], [2]

P

PATH, [1], [2], [3], [4] PercentStrategy Private

py.test command line option --repeat <number> -h, --help PYTHONPATH, [1], [2], [3], [4], [5], [6], [7], [8], [9]

R

read() (omero.grid.Table method) Read-annotate Read-only Read-write readCoordinates() (omero.grid.Table method)

Remove annotations Render RequestEvent ResponseEvent Restricted Administrators rowNumbers (omero.grid.Data attribute)

S

setAllMetadata() (omero.grid.Table method) setMetadata() (omero.grid.Table method) setup.py-test command line option --markers -h, --help -k <string> -m <marker> -s -t <test_path>, --test-path <test_path>

slice() (omero.grid.Table method) SLICEPATH, [1] StateChangeEvent Sudo

U

update() (omero.grid.Table method)

Upload Scripts

V

values (omero.grid.DoubleColumn attribute)

VERBOSE View

W

Write Data