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1 The Open Microscopy Environment A DataBase for the storage and manipulation of image data Michal Kuneš xkunes@utia.cas.cz ZOI UTIA, ASCR, Friday seminar
2 OMERO 2
3 What is OMERO? From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software (Matlab,...). Images are stored locally on the server in binary repository. 3
4 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 4
5 The Bio-Formats Library - a Java library for readingand writing biological image files. - a software tool for reading and writing image data using standardized, open formats. - Currently reads and converts more than 120 file formats to the OME-TIFF data standard. - supports SW like: ImageJ, CellProfiler, Icy, OMERO, JCB DataViewer, Matlab. 5
6 Licenses All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under: or through GNU public "copyleft" licenses commercial license from Glencoe Software. 6
7 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming / SW Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 7
8 OMERO.server Installation prerequisites: - Java (JDK) (EULA) - Python (PyWin, PIL) (Open source) - ICE (The Internet Communications Engine) (O. s. under GPL) - PostgreSQL (Open source) 8
9 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 9
10 OMERO.web - an integral part of the OMERO platform - management, viewing, attachment and association of files to images, datasets, and projects from the OMERO.server (+ webadmin) - IIS 5.1, 6.0 or 7.0 on Microsoft Windows (since OMERO 4.2.1) - FastCGI using a FastCGI capable web server such as Apache, nginx or lighttpd - the built-in Django lightweight development server (for testing only) - a similar view to the OMERO.insight (next slides) 10
11 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 11
12 OMERO.importer - JAVA based application for image importing into OMERO.server 12
13 Project and Dataset selection: OMERO.importer 13
14 OMERO.importer 14
15 OMERO.importer Adding tags at import To archive data files in their original format on the OMERO server click the Archive checkbox. 15
16 OMERO.importer The progress of imports is shown in the Import tab. 16
17 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 17
18 OMERO.insight Connecting to database and start 18
19 OMERO.insight 19
20 Import Data from OMERO.insight OMERO.insight 20
21 Viewing Data OMERO.insight 21
22 Viewing Data... OMERO.insight
23 Viewing Data... - Metadata OMERO.insight
24 Managing Data... OMERO.insight - Description, Stars
25 Managing Data... OMERO.insight - Tags + filters
26 Collaborating with Data - User administration - 3 types of Groups OMERO.insight
27 ROI - Regions of Interest - ROI selector - draw rectangle, ellipse, point, line, polygon - add a text ROI - show/hide text You can: - save ROIs - load ROIs - open the ROI assistant (propagate through Z stack or time sequence) - delete ROIs - Intensity View (for the ROI) OMERO.insight
28 OMERO.insight Exporting Images as: - OME-TIFF - JPEG, PNG or TIFF - original image format (if it was archived at import) Using Scripts to Export Images
29 OMERO.insight Using Scripts to Export Images Batch Image Export - Saves multiple images as in a zip Make Movie - Creates a movie (z stacks and t sequences) Movie Figure Movie ROI Figure ROI Split Figure Split View Thumbnail Thumbnail Figure 29
30 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 30
31 OMERO.editor It has been designed to achieve two key functions: - Facilitate the digital recording of experimental metadata. - It saves metadata as XML files that can be used to annotate images, datasets etc. - Enable important parameters to be distinguished from the main text, e.g. to summarise the experiment in a concise form. Usage: 1. Preparation of a Protocol - Multiple parameters per step 2. Creating a Experiment from the protocol 3. Annotating images / datasets
32 OMERO.editor Displays a single file per window, which will typically be split into 3 panels. Text View of a protocol: 32
33 Tree View of a protocol: OMERO.editor define an Experiment 33
34 A Experiment data: OMERO.editor Table of parameter values 34
35 OMERO.editor Protocol / Experiment - Save As (to server)
36 OMERO.editor Protocol / Experiment preview on OMERO.server in OMERO.insight: 36
37 OMERO.editor Protocols / Experiments can be connected throw each other and to images: 37
38 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 38
39 1. 2. OMERO and ImageJ
40 OMERO and ImageJ / FIJI Windows 7 example 40
41 OMERO JAVA applications: - OMERO.server Clients: - OMERO.web - OMERO.importer - OMERO.insight - OMERO.editor Programming Interface: - C++ - Java, ImageJ plugin - Matlab - Python - Command line interface - Dropbox + OMERO.tables (+ HDF5, NumPy, PyTables), Bio-Formats Library 41
42 OMERO and Matlab Matlab toolbox: >> loadomero.m Define a client and session close session and clear memory on the end. 42
43 OMERO and Matlab example 43
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