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The Open Microscopy Environment
A DataBase for the storageand manipulation of image data
Michal Kuneš[email protected]
ZOI UTIA, ASCR, Friday seminar 13.12.2013
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OMERO
http://www.openmicroscopy.org 2
http://www.openmicroscopy.org/site/support/omero4/users/index.html
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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.
http://www.openmicroscopy.org 3
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OMEROJAVA 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
http://www.openmicroscopy.org 4
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The Bio-Formats Library
http://www.openmicroscopy.org/site/products/bio-formats
- 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 formatsto the OME-TIFF data standard.
- supports SW like: ImageJ, CellProfiler, Icy, OMERO, JCB DataViewer,
Matlab.
http://www.openmicroscopy.org 5
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Licenses
All OME formats and software are freely available, and all OMERO and
Bio-Formats source code is available under:
GNU public "copyleft" licenses
or through
commercial license from Glencoe Software.
http://www.openmicroscopy.org 6
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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
http://www.openmicroscopy.org 7
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OMERO.server
Installation prerequisites:
- Java (JDK) (EULA)
- Python (PyWin, PIL) (Open source)
- ICE 3.2-3.4 (The Internet Communications Engine) (O. s. under GPL)
- PostgreSQL (Open source)
http://www.openmicroscopy.org 8
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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
http://www.openmicroscopy.org 9
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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)
http://www.openmicroscopy.org 10
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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
http://www.openmicroscopy.org 11
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OMERO.importer
- JAVA based application for image importing into OMERO.server
http://www.openmicroscopy.org 12
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OMERO.importer
http://www.openmicroscopy.org 13
Project and Dataset selection:
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OMERO.importer
http://www.openmicroscopy.org 14
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OMERO.importer
http://www.openmicroscopy.org 15
To archive data files
in their original format
on the OMERO server
click the Archive
checkbox.
Adding tags at import
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OMERO.importer
http://www.openmicroscopy.org 16
The progress of imports is shown in the Import tab.
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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
http://www.openmicroscopy.org 17
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OMERO.insight
http://www.openmicroscopy.org 18
Connecting to database and start
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OMERO.insight
http://www.openmicroscopy.org 19
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OMERO.insight
http://www.openmicroscopy.org 20
Import Data from OMERO.insight
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OMERO.insight
http://www.openmicroscopy.org 21
Viewing Data
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OMERO.insight
http://www.openmicroscopy.org 22
Viewing Data ....
http://help.openmicroscopy.org/viewing-data.html
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OMERO.insight
http://www.openmicroscopy.org 23
Viewing Data ....
http://help.openmicroscopy.org/viewing-data.html
- Metadata
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OMERO.insight
http://www.openmicroscopy.org 24
Managing Data ....
- Description, Stars
http://help.openmicroscopy.org/managing-data.html
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OMERO.insight
http://www.openmicroscopy.org 25
Managing Data ....
http://help.openmicroscopy.org/managing-data.html
- Tags + filters
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OMERO.insight
http://www.openmicroscopy.org 26
- User administration
- 3 types of Groups
Collaborating with Data
http://help.openmicroscopy.org/collaboration.html
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OMERO.insight
http://www.openmicroscopy.org 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)
http://help.openmicroscopy.org/measurement-tool.html
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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
....
http://www.openmicroscopy.org 28
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OMERO.insightUsing 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
http://www.openmicroscopy.org 29
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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
http://www.openmicroscopy.org 30
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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
http://www.openmicroscopy.org 31http://help.openmicroscopy.org/editor.html
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OMERO.editorDisplays a single file per window, which will typically be split into 3 panels.
Text View of a protocol:
http://www.openmicroscopy.org 32
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OMERO.editorTree View of a protocol: define an Experiment
http://www.openmicroscopy.org 33
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OMERO.editorA Experiment data:
http://www.openmicroscopy.org 34
Table of parameter values
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OMERO.editorProtocol / Experiment - Save As (to server) ...
http://www.openmicroscopy.org 35
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OMERO.editorProtocol / Experiment preview on OMERO.server in OMERO.insight:
http://www.openmicroscopy.org 36
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OMERO.editorProtocols / Experiments can be connected throw each other and to images:
http://www.openmicroscopy.org 37
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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
http://www.openmicroscopy.org 38
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OMERO and ImageJ
http://www.openmicroscopy.org 39
1. 2.
3.
4. ...
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OMERO and ImageJ / FIJI
http://www.openmicroscopy.org 40Windows 7 example
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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
http://www.openmicroscopy.org 41
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OMERO and Matlab
Matlab toolbox:>> loadOmero.m
Define a client and session ...
... close session and clear memory on the end.
http://www.openmicroscopy.org 42
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OMERO and Matlab example
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