Key Features of OMERO

Analyze your data in OMERO

Analysis apps can access images on OMERO and save results back to the server.

OMERO.scripts run on the server itself and can be launched from the clients.

Connecting analytical apps to OMERO

Powerful 3rd party analytical tools can analyze your images stored in OMERO.

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Attaching analytical results

Support for storing analytical results attached to images.

View User Guide View guide for large data

Draw ROIs

Draw ROIs across multiple dimensions and measure pixel intensity.

View user guide More about OMERO.iviewer

ImageJ/Fiji plugin

Import images and save ROIs, overlays and analysis results from ImageJ/Fiji into OMERO.

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Scripting service

Write scripts to add functionality to OMERO.server and share them with the community.

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Python and OMERO

An easy-to-use API for OMERO making it easier to work with your data in Python.

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OMERO.matlab toolbox

Work with your OMERO data in MATLAB using a plugin.

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Java and OMERO

Connect to OMERO using Java API.

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R and OMERO

Connect to OMERO in R using rJava and the OMERO Java Gateway.

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Tabular Data support

HDF-based storage of measurement results with an API for exporting to Excel using OMERO.tables.

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OMERO.mtools

An optional suite of MATLAB-based image analysis tools.

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ROI Folders

Organize ROIs into hierarchical folders for viewing and analysis.

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Add functionality to your OMERO installation with community-developed optional apps and plugins

Orbit Image Analysis

Whole Slide Image analysis that connects to OMERO.

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QuPath

Quantitative Pathology and Bioimage Analysis that connects to OMERO.

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CellProfiler

Quantitative analysis of biological images that connects to OMERO.

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ilastik

An interactive learning and segmentation toolkit that connects to OMERO.

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OMERO-WND-CHARM

Scripts for using WND-CHARM, an image classifier, on images stored in OMERO.

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KNIME-OMERO integration

Start OMERO.insight directly within KNIME for image processing.

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FlIMfit

FLIM analysis package that connects to OMERO.

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