6- OMERO & Orbit

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Orbit Image Analysis software (Actelion Pharmaceuticals Ltd) has been developed for whole slide image analysis. An open-source version has been released for common use under the GPL license.

Orbit allows to automatize image analysis tasks that were previously exclusively performed manually by the scientist, such as counting cells, detecting and counting specific type of cells, quantifying the amount of a stained tissue type, etc

Its main focus is to perform machine learning based classification and segmentation making use of multi resolution image pyramids.


1- Install and configure Orbit to access Omero server

Depending on your computer OS, go to http://www.orbit.bio/download/ and download the corresponding Orbit version. Please make sure following the entire instructions.

a- when you run Orbit for the first time, you need to set-up the Omero server ‘s host adress at “omero.icm-institute.org”


b- enter your ICM logins.


c- open images from Omero server by clicking on ‘Open Image from Server’ or by exploring your data home/groups from the directory tree in the top left part of the screen. Select the image by double click.


d- Now, the image is loaded from the Omero repository to Orbit. you can start classification, segmentations …


2- Orbit’s main features:


More Complete user manual is available here and you can visit the website on http://www.orbit.bio/