Index

Symbols

$OMERODIR --advanced-help omero-import command line option --all omero-help command line option --archived omero-fs-images command line option --bulk omero-import command line option --cache omero-fs-importtime command line option --check omero-fs-sets command line option --debug omero-import command line option --depth omero-import command line option --description omero-import command line option --dry-run omero-chgrp command line option omero-chown command line option omero-delete command line option --email omero-import command line option --errs 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 --file omero-import 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 --group omero-login command line option --groups omero-fs-usage command line option --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 pytest command line option --include omero-chgrp command line option omero-chown command line option omero-delete command line option --iterate omero-export command line option --java-help omero-import command line option --key omero-login command line option --limit omero-fs-images command line option omero-fs-sets command line option --list omero-help command line option --logprefix omero-import command line option --logs omero-import command line option --managed omero-fs-repos command line option --markers pytest command line option --name omero-import command line option --no-move omero-fs-rename command line option --offset omero-fs-images command line option omero-fs-sets command line option --order 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 --output omero-import command line option --parallel-fileset omero-import command line option --parallel-upload omero-import command line option --parents omero-fs-mkdir command line option --password omero-login command line option --port omero-login command line option --recursive omero-help 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 --server omero-login command line option --size_only omero-fs-usage command line option --skip omero-import command line option --style 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 omero-login command line option --summary omero-fs-importtime command line option --target omero-import command line option --units omero-fs-usage command line option --upload omero-import command line option --user omero-login command line option --wait omero-fs-usage command line option --with-transfer omero-fs-sets command line option --without-images omero-fs-sets command line option -d 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 omero-import command line option omero-login command line option -h 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 pytest command line option -k omero-login command line option pytest command line option -m pytest command line option -n omero-import command line option -p omero-import command line option omero-login command line option -r omero-import command line option -s omero-import command line option omero-login command line option pytest command line option -T omero-import command line option -u omero-import command line option omero-login command line option -w omero-login command line option -x omero-import command line option

A

Action Add Users to Groups addData() (omero.grid.Table method) admin (omero.query.timeout property) Administrator admins (omero.web property) Analyst

analyzer (omero.search property) Annotate append (omero.jvmcfg property) application_server (omero.web property) apps (omero.web property) auth (omero.mail.smtp property) authority (omero.db property)

B

background_threads (omero.threads property) background_timeout (omero.threads property) backoff (omero.pixeldata property) base (omero.ldap property) base_include_template (omero.web property) batch (omero.pixeldata property) (omero.search property)

bean (omero.mail property) (omero.metrics property) (omero.policy property) binary_access (omero.policy property) bitand (omero.security.filter property) bridges (omero.search property) broken

C

caches (omero.web property) cancel_timeout (omero.threads property) center_plugins (omero.web.ui property) ch.qos.logback.core.Appender.error Change ownership Chgrp chmod_strategy (omero.security property) Chown chunk_size (omero.web property) Ciphers (omero.glacier2.IceSSL property) class (omero.mail.smtp.socketFactory property) client_downloads_base (omero.web.login property) 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) config (omero.ldap property) (omero.mail property) connect_timeout (omero.ldap property) connection omero-login command line option connectiontimeout (omero.mail.smtp property) cors_origin_allow_all (omero.web property) cors_origin_whitelist (omero.web property) Create and Edit Groups Create and Edit Users cron (omero.pixeldata property) (omero.scripts.cache property) (omero.search property) csrf_cookie_httponly (omero.web property) csrf_cookie_samesite (omero.web property) csrf_cookie_secure (omero.web property) csrf_trusted_origins (omero.web property) CXX CXXFLAGS, [1]

D

Data Viewer databases (omero.web property) db (omero.cluster.read_only property) debug (omero.mail.smtp property) (omero.web property) default (omero.pixeldata.backoff property) default_group (omero.web.search property) default_user (omero.web.search property) Delete Delete Data

description (omero.client.ui.tree.orphans property) dialect (omero.db property) dir (omero.data property) (omero.managed property) (omero.pixeldata.memoizer property) directory (omero.logging property) dispose (omero.pixeldata property) django_additional_settings (omero.web property) driver (omero.db property) DYLD_LIBRARY_PATH, [1]

E

Edit enable (omero.mail.smtp.starttls property) enabled (omero.client.ui.menu.dropdown.colleagues property) (omero.client.ui.menu.dropdown.everyone property) (omero.client.ui.menu.dropdown.leaders property) (omero.client.ui.tree.orphans property) (omero.web.feedback.comment property) (omero.web.feedback.error property) (omero.web.public property) (omero.web.public.cache property) environment variable $OMERODIR CMAKE_INCLUDE_PATH, [1] CMAKE_LIBRARY_PATH CXX CXXFLAGS, [1] DYLD_LIBRARY_PATH, [1] GTEST_ROOT ICE_CONFIG, [1], [2], [3], [4], [5], [6], [7] ICE_HOME, [1] JAVA_OPTS LD_LIBRARY_PATH, [1] OMERO_CONFIG OMERO_HOME, [1], [2], [3], [4], [5], [6], [7] OMERO_PASSWORD OMERO_PREFIX, [1], [2] OMERO_SESSION_DIR, [1], [2] OMERO_SESSIONDIR, [1], [2], [3], [4] OMERO_TMPDIR, [1], [2], [3], [4] OMERO_USERDIR, [1], [2] OMERODIR, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] PATH, [1], [2] PYTHONPATH, [1], [2] SLICEPATH, [1] VERBOSE

error (omero.throttling.method_time property) event_log_loader (omero.pixeldata property) (omero.search property) excludes (omero.search property)

F

fallback (omero.mail.smtp.socketFactory property) favicon_url (omero.web property)

feedback (omero.qa property) from (omero.mail property)

G

get_only (omero.web.public property) 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)

graphite (omero.metrics property) Group and Data Organizer Group member Group owner group_filter (omero.ldap property) group_mapping (omero.ldap property) GTEST_ROOT

H

heap_dump (omero.jvmcfg property) heap_size (omero.jvmcfg property) host (omero.client.web property) (omero.db property) (omero.mail property) (omero.web.application_server property)

html_meta_referrer (omero.web property)

I

ICE_CONFIG, [1], [2], [3], [4], [5], [6], [7] ICE_HOME, [1] IceSSL (omero.glacier2 property) icetransports (omero.client property) idle_timeout (omero.threads property) ignore_case (omero.security property) Importer include_actions (omero.search property)

include_types (omero.search property) index_template (omero.web property) indexer (omero.throttling.method_time.error property) (omero.throttling.method_time.warn property) initial_zoom_level (omero.client.viewer property) initialize() (omero.grid.Table method) interpolate_pixels (omero.client.viewer property) IPv6 (Ice property)

J

JAVA_OPTS jvm.fileDescriptorCountRatio

jython (omero.launcher property) (omero.process property)

K

key (omero.web.public.cache property)

keyStore (omero.security property) keyStorePassword (omero.security property)

L

label (omero.client.ui.menu.dropdown.colleagues property) (omero.client.ui.menu.dropdown.everyone property) (omero.client.ui.menu.dropdown.leaders property) lastModification (omero.grid.Data attribute) LD_LIBRARY_PATH, [1] level (omero.logging property) local (omero.pixeldata.memoizer.dir property) locking_strategy (omero.search property)

logdir (omero.web property) login_failure_throttle_count (omero.security property) login_failure_throttle_time (omero.security property) login_incorrect_credentials_text (omero.web property) login_logo (omero.web property) login_redirect (omero.web property) login_view (omero.web property) lognum (omero.logging property) logsize (omero.logging property)

M

ManualStrategy matlab (omero.launcher property) (omero.process property) max_file_size (omero.search property) max_fileset_size (omero.search property) max_partition_size (omero.search property) max_plane_float_override (omero.pixeldata property) max_plane_height (omero.pixeldata property) max_plane_width (omero.pixeldata property) max_projection_bytes (omero.pixeldata property) max_requests (omero.web.application_server property) max_size (omero.client.download_as property) max_system_memory (omero.jvmcfg property) max_table_download_rows (omero.web property)

max_threads (omero.threads property) max_user_time_to_idle (omero.sessions property) max_user_time_to_live (omero.sessions property) maximum (omero.sessions property) maximum_multifile_download_size (omero.web property) maxpixels (omero.pixeldata.backoff property) memoizer_wait (omero.pixeldata property) merge_factor (omero.search property) metadata_panes (omero.web.ui property) middleware (omero.web property) min_system_memory (omero.jvmcfg property) min_threads (omero.threads property) Mix data Move between groups

N

name (omero property) (omero.client.ui.tree.orphans property) (omero.db property)

new_user_group (omero.ldap property) new_user_group_owner (omero.ldap property) nginx_server_extra_config (omero.web property) nodedescriptors (omero.server property)

O

objects_read_interval (omero.throttling property) objects_written_interval (omero.throttling property) ome.io.nio.PixelsService.minmaxTimes ome.io.nio.PixelsService.tileTimes ome.services.eventlogs.EventLogQueue.priorityCount omero-admin-start command line option --force-rewrite --foreground --help -h omero-admin-stop command line option --force-rewrite --help -h 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 omero-fs-images command line option --archived --extended --help --limit --offset --order --style -h omero-fs-importtime command line option --cache --summary omero-fs-mkdir command line option --help --parents -h omero-fs-rename command line option --help --no-move -h omero-fs-repos command line option --help --managed --style -h omero-fs-sets command line option --check --extended --help --limit --offset --order --style --with-transfer --without-images -h omero-fs-usage command line option --groups --help --report --size_only --style --units --wait -h

omero-help command line option --all --list --recursive omero-import command line option --advanced-help --bulk --debug --depth --description --email --errs --file --help --java-help --logprefix --logs --name --output --parallel-fileset --parallel-upload --report --skip --target --upload -d -f -g -h -n -p -r -s -T -u -x omero-login command line option --group --key --password --port --server --sudo --user -g -k -p -s -u -w connection 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.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_CONFIG OMERO_HOME, [1], [2], [3], [4], [5], [6], [7] OMERO_PASSWORD OMERO_PREFIX, [1], [2] OMERO_SESSION_DIR, [1], [2] OMERO_SESSIONDIR, [1], [2], [3], [4] OMERO_TMPDIR, [1], [2], [3], [4] OMERO_USERDIR, [1], [2] OMERODIR, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] open_with (omero.web property) opengraph (omero.web.sharing property)

P

page_size (omero.web property) pass (omero.db property) password (omero.ldap property) (omero.mail property) (omero.web.public property) password_provider (omero.security property) password_required (omero.security property) patch (omero.db property) PATH, [1], [2] path (omero.fs.repo property) path_rules (omero.fs.repo property) percent (omero.jvmcfg property) PercentStrategy perm_gen (omero.jvmcfg property) ping_interval (omero.web property) pipeline_css_compressor (omero.web property) pipeline_js_compressor (omero.web property) pipeline_staticfile_storage (omero.web property) plate_layout (omero.web property) poolsize (omero.db property) port (omero.db property) (omero.mail property) (omero.mail.smtp.socketFactory property) (omero.web.application_server property)

prefix (omero.ports property) (omero.web property) prepared_statement_cache_size (omero.db property) Private profile (omero.db property) properties (omero.db property) protocol (omero.mail.transport property) Protocols (omero.glacier2.IceSSL property) ProtocolVersionMax (omero.glacier2.IceSSL property) pytest command line option --help --markers -h -k -m -s python (omero.launcher property) (omero.process property) PYTHONPATH, [1], [2]

R

ram_buffer_size (omero.search property) read() (omero.grid.Table method) Read-annotate Read-only Read-write read_only (omero.cluster property) read_timeout (omero.ldap property) readCoordinates() (omero.grid.Table method) redirect_allowed_hosts (omero.web property) redirector (omero.cluster property) referral (omero.ldap property) registry (omero.ports property)

registry_timeout (omero.grid property) Remove annotations Render repetitions (omero.pixeldata property) (omero.search property) repo (omero.cluster.read_only property) reporting_loops (omero.search property) Restricted Administrators right_plugins (omero.web.ui property) roi_limit (omero.client.viewer property) root_application (omero.web property) rowNumbers (omero.grid.Data attribute)

S

scripts_to_ignore (omero.client property) secret_key (omero.web property) secure (omero.web property) secure_proxy_ssl_header (omero.web property) servants_per_session (omero.throttling property) server_id (omero.web.public property) server_list (omero.web property) session_cookie_age (omero.web property) session_cookie_domain (omero.web property) session_cookie_name (omero.web property) session_cookie_path (omero.web property) session_cookie_samesite (omero.web property) session_cookie_secure (omero.web property) session_engine (omero.web property) session_expire_at_browser_close (omero.web property) session_serializer (omero.web property) setAllMetadata() (omero.grid.Table method) setMetadata() (omero.grid.Table method)

show_client_downloads (omero.web.login property) show_forgot_password (omero.web property) slf4j_minutes (omero.metrics property) slice() (omero.grid.Table method) SLICEPATH, [1] spec (omero.scripts.cache property) sql_action_class (omero.db property) ssl (omero.ports property) static_root (omero.web property) static_url (omero.web property) staticfile_dirs (omero.web property) statistics (omero.db property) strategy (omero.jvmcfg property) Sudo supported (omero.checksum property) sync_force (omero.sessions property) sync_interval (omero.sessions property) sync_on_login (omero.ldap property) system_memory (omero.jvmcfg property)

T

tcp (omero.ports property) template_dirs (omero.web property) threads (omero.pixeldata property) thumb_default_size (omero.client.browser property) thumbnails_batch (omero.web property) tile_height (omero.pixeldata property) tile_sizes_bean (omero.pixeldata property) tile_width (omero.pixeldata property) time_zone (omero.web property) timedlog (omero.logging property) timeout (omero.mail.smtp property) (omero.query property) (omero.scripts property) (omero.sessions property) (omero.web.public.cache property)

top_links (omero.web.ui property) top_logo (omero.web property) top_logo_link (omero.web property) trustStore (omero.security property) trustStorePassword (omero.security property) twitter (omero.web.sharing property) type_order (omero.client.ui.tree property)

U

update() (omero.grid.Table method) Upload Scripts url (omero.db property) url_filter (omero.web.public property) urls (omero.ldap property) use_x_forwarded_host (omero.web property)

user (omero.db property) (omero.web.public property) user_dropdown (omero.web property) user_filter (omero.ldap property) user_mapping (omero.ldap property) username (omero.ldap property) (omero.mail property)

V

values (omero.grid.DoubleColumn attribute) VERBOSE VerifyPeer (omero.glacier2.IceSSL property)

version (omero.db property) View view (omero.web.viewer property)

W

warn (omero.throttling.method_time property) webgateway_cache (omero.web property) Write Data ws (omero.ports property)

wsgi_args (omero.web property) wsgi_timeout (omero.web property) wsgi_workers (omero.web property) wss (omero.ports property)

X

x_frame_options (omero.web property)