prezentace omero v06 - caszoi.utia.cas.cz/files/_prezentace_omero_v06.pdf · microsoft powerpoint -...

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

OMERO

http://www.openmicroscopy.org 2

http://www.openmicroscopy.org/site/support/omero4/users/index.html

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.


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


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.


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.


OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor

Programming / SW Interface:

- C++


- Matlab

- Python


- Dropbox



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)


OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor


- C++


- Matlab

- Python


- Dropbox



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)


OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor


- C++


- Matlab

- Python


- Dropbox



OMERO.importer

- JAVA based application for image importing into OMERO.server


OMERO.importer


Project and Dataset selection:

OMERO.importer


OMERO.importer


To archive data files

in their original format

on the OMERO server

click the Archive

checkbox.

Adding tags at import

OMERO.importer


The progress of imports is shown in the Import tab.

OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor


- C++


- Matlab

- Python


- Dropbox



OMERO.insight


Connecting to database and start

OMERO.insight


OMERO.insight


Import Data from OMERO.insight

OMERO.insight


Viewing Data

OMERO.insight


Viewing Data ....

http://help.openmicroscopy.org/viewing-data.html

OMERO.insight


Viewing Data ....

http://help.openmicroscopy.org/viewing-data.html

- Metadata

OMERO.insight


Managing Data ....

- Description, Stars

http://help.openmicroscopy.org/managing-data.html

OMERO.insight


Managing Data ....

http://help.openmicroscopy.org/managing-data.html

- Tags + filters

OMERO.insight


- User administration

- 3 types of Groups

Collaborating with Data

http://help.openmicroscopy.org/collaboration.html

OMERO.insight


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

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

....


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


OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor


- C++


- Matlab

- Python


- Dropbox



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

OMERO.editorDisplays a single file per window, which will typically be split into 3 panels.

Text View of a protocol:


OMERO.editorTree View of a protocol: define an Experiment


OMERO.editorA Experiment data:


Table of parameter values

OMERO.editorProtocol / Experiment - Save As (to server) ...


OMERO.editorProtocol / Experiment preview on OMERO.server in OMERO.insight:


OMERO.editorProtocols / Experiments can be connected throw each other and to images:


OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor


- C++


- Matlab

- Python


- Dropbox



OMERO and ImageJ


1. 2.

3.

4. ...

OMERO and ImageJ / FIJI

http://www.openmicroscopy.org 40Windows 7 example

OMERO

JAVA applications:

- OMERO.server

Clients:


- OMERO.insight

- OMERO.editor


- C++


- Matlab

- Python


- Dropbox



OMERO and Matlab

Matlab toolbox:>> loadOmero.m

Define a client and session ...

... close session and clear memory on the end.


OMERO and Matlab example


prezentace omero v06 - caszoi.utia.cas.cz/files/_prezentace_omero_v06.pdf · microsoft powerpoint -...

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