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OMERO Documentation Release 5.2.5

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OMERO Documentation Release 5.2.5 OMERO Documentation Release 5.2.5 The Open Microscopy Environment July 29, 2016 CONTENTS I About the OMERO Platform 2 1 Introduction 3 2 OMERO clients 4 2.1 OMERO clients overview .............................................. 4 2.2 Command Line Interface as an OMERO client ................................... 6 3 Additional resources 24 3.1 Community support ................................................. 24 3.2 What’s new for OMERO 5.2 for users ........................................ 25 3.3 OMERO version history ............................................... 25 4 Quickstart server access 42 4.1 OMERO demo server ................................................ 42 4.2 OMERO virtual appliance .............................................. 45 II System Administrator Documentation 60 5 Server Background 61 5.1 What’s new for OMERO 5.2 for sysadmins ..................................... 61 5.2 Server overview ................................................... 61 5.3 System requirements ................................................. 62 5.4 Version requirements ................................................. 64 5.5 Example production server set-ups .......................................... 76 5.6 Known limitations .................................................. 78 5.7 Groups and permissions system ........................................... 80 6 Server Installation and Maintenance 85 6.1 Server installation on UNIX (and UNIX-like platforms) .............................. 85 6.2 Server installation on Windows ........................................... 145 6.3 Command Line Interface as an OMERO admin tool ................................ 173 6.4 Upgrading and maintenance ............................................. 184 6.5 Installing additional features ............................................. 195 6.6 Troubleshooting OMERO .............................................. 207 7 Optimizing Server Configuration 214 7.1 Server security and firewalls ............................................. 214 7.2 LDAP authentication ................................................. 217 7.3 Performance and monitoring ............................................. 221 7.4 Search and indexing configuration .......................................... 225 7.5 FS configuration options ............................................... 228 7.6 Grid configuration .................................................. 230 7.7 Setting the OMERO_HOME environment variable ................................. 233 7.8 Configuration properties glossary .......................................... 234 7.9 Syslog configuration ................................................. 259 8 Optimizing OMERO as a Data Repository 262 i 8.1 Customize OMERO clients ............................................. 262 8.2 Public data in the repository ............................................. 266 9 Data Import and Storage 268 9.1 OMERO.dropbox ................................................... 268 9.2 In-place import .................................................... 273 9.3 Advanced import scenarios ............................................. 280 III Developer Documentation 285 10 Introduction to OMERO 287 10.1 What’s new for OMERO 5.2 for developers ..................................... 287 10.2 Installing OMERO from source ........................................... 288 10.3 Build System ..................................................... 289 10.4 Working with OMERO ................................................ 293 10.5 Running and writing tests .............................................. 299 11 Using the OMERO API 308 11.1 OMERO Python language bindings ......................................... 308 11.2 Blitz Gateway documentation ............................................ 328 11.3 Command Line Interface as an OMERO development tool ............................. 332 11.4 OMERO Java language bindings ........................................... 334 11.5 OMERO MATLAB language bindings ....................................... 347 11.6 OMERO C++ language bindings ........................................... 362 12 Analysis 369 12.1 Local analysis .................................................... 369 12.2 Storing external data in OMERO .......................................... 369 12.3 OMERO.tables .................................................... 370 13 Scripts - plugins for OMERO 376 13.1 Introduction to OMERO.scripts ........................................... 376 13.2 OMERO.scripts user guide .............................................. 379 13.3 Guidelines for writing OMERO.scripts ....................................... 385 13.4 MATLAB and Python ................................................ 388 13.5 OMERO.scripts advanced topics ........................................... 390 14 Web 394 14.1 OMERO.web framework ............................................... 394 14.2 OMERO.web deployment for developers ...................................... 397 14.3 Creating an app .................................................... 398 14.4 Webclient Plugins .................................................. 403 14.5 Editing OMERO.web ................................................. 408 14.6 WebGateway ..................................................... 409 14.7 Embedding an OMERO.web viewport in a web page ................................ 413 14.8 Writing OMERO.web views ............................................. 414 14.9 Writing page templates in OMERO.web ....................................... 418 14.10 Cross Site Request Forgery protection ........................................ 421 14.11 The OMERO.web client application ......................................... 422 15 Insight 424 15.1 Architecture ..................................................... 424 15.2 Configuration ..................................................... 426 15.3 Contributing to OMERO.insight ........................................... 431 15.4 Directory contents .................................................. 431 15.5 Event bus ....................................................... 432 15.6 Event ......................................................... 433 15.7 How to build an agent ................................................ 436 15.8 How to build an agent’s view ............................................. 439 15.9 Retrieve data from server ............................................... 441 15.10 Organization ..................................................... 445 ii 15.11 Taskbar ........................................................ 446 16 More on API Usage 452 16.1 Developing OMERO clients ............................................. 452 16.2 OMERO Application Programming Interface .................................... 488 16.3 OMERO admin interface ............................................... 491 16.4 Deleting in OMERO ................................................. 492 16.5 OMERO Import Library ............................................... 494 16.6 TempFileManager .................................................. 495 16.7 Exception handling .................................................. 496 16.8 Omero logging .................................................... 502 16.9 Using the new 5.1 graph requests .......................................... 504 17 The OME Data Model 507 17.1 OME-Remote Objects ................................................ 507 17.2 Structured annotations ................................................ 517 17.3 Glossary of all OMERO Model Objects ....................................... 520 17.4 Units ......................................................... 579 17.5 Key-value pairs .................................................... 582 17.6 Available transformations .............................................. 584 18 Searching 586 18.1 OMERO search .................................................... 586 18.2 File parsers ...................................................... 589 18.3 Search bridges .................................................... 590 19 Authentication and Security 593 19.1 Password Provider .................................................. 593 19.2 LoginAttemptListener ................................................ 594 19.3 LDAP plugin design ................................................. 594 19.4 OMERO roles .................................................... 595 19.5 OMERO security system ............................................... 596 19.6 OMERO permissions history, querying and usage .................................. 600 20 OMERO.server in depth 609 20.1 OMERO.server overview ............................................... 609 20.2 Extending OMERO.server .............................................. 610 20.3 OMERO.blitz ..................................................... 617 20.4 OMERO.fs ...................................................... 618 20.5 Import under OMERO.fs ............................................... 618 20.6 OMERO.processor .................................................. 622 20.7 OMERO.server image rendering ........................................... 623 20.8 Clustering ...................................................... 623 20.9 Collection counts ................................................... 624 20.10 How To create a service ............................................... 625 20.11 OMERO sessions ................................................... 626 20.12 Aspect-oriented programming ............................................ 629 20.13
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