Figure 13: A Workflow for processing images from OMERO
This section describes the modules of the ProStack image processing platform that make it possible to communicate with OMERO on the GNU/Linux operating system. The guide is targeted at the scientists that store experimental images in OMERO and need to process those images with complex scenarios.
It is assumed that OMERO and ProStack software are properly installed and run in production mode at user’s site, the user has some images in OMERO and is able to use OMERO client programms. Installation and configuration procedures are not described here.
It is assumed that a reader is able to run scripts from a command line, set environment variables up and understand the basics of the client-server software architecture. These terms and actions are not explained here.
The authors are not affiliated in any way with OMERO Team nor any of the latter is affiliated with ProStack Team. The solution described here was developed using publicly available information and source code.
The modules to communicate with OMERO are currently included in the following ProStack distributions starting from version 2.5.1:
Though both ProStack and OMERO work on Microsoft Windows the modules described here were not tested on this platform. This means that they may or may not work there. If a reader is eager to test the software he may contact the authors for further information and explanation of known problems.
The OMERO software is written in Java and requires Java 1.5. It is sufficient if standard OMERO clients run on your machine. The ProStack modules were developed in Java and tested with OMERO platform v4.1 and the distribution includes Java libraries from OMERO clients distribution.
There are four ProStack modules for interaction with OMERO: file, omero_exporter, omero_exporter_i and omero_importer. The first three are used to get the image data from the OMERO server and the last one uploads the processing results. The user credentials are specified for each of the module manually and verified on each connection. The user should be aware that the credentials are saved in the scenario in clear text.
If non of the operators is selected in the main window the middle click in the scenario builder inserts the node ’file’. If ProStack modules for OMERO are correctly installed the options dialog for ’file’ node contains the button ’Network’ in the bottom-right corner.
This operator downloads the requested image from OMERO server. It uses Java OMERO Client API for communication and saves the image in OME-TIFF format. The path to the image from OMERO server root, i.e. the Project, Dataset and Image names should be provided by the node linked to the input port of omero_exporter. The node ’file’ provides such functionality.
input
1 image:.tif
output
1 image:.tif
parameters
Host – the hostname of the OMERO server,
Port – the port number that OMERO server is listening on (usually - 4063),
Login – user name,
Password
This operator downloads the requested image from OMERO server. It uses Java OMERO Client API for communication and saves the image in OME-TIFF format. The path to the image from OMERO server root, i.e. the Project, Dataset and Image names are the options of this operator and need to be defined manually.
output
1 image:.tif
parameters
Host – the hostname of the OMERO server,
Port – the port number that OMERO server is listening on (usually - 4063),
Login – user name,
Password,
Project,
Dataset,
Image
This operator uploads an input image to OMERO server. It uses command line importer from OMERO Clients suite.
input
1 image:.tif
parameters
Host – the hostname of the OMERO server,
Port – the port number that OMERO server is listening on (usually - 4063),
Login – user name,
Password,
Dataset – the numeric id of the dataset,
Image
We will start with the new workspace and build a scenario shown in 13 that fetches the 3D image from OMERO server, computes the maximal projection and stores the resulting image back to the server. The image represents the nuclei in Drosophila embryo.
First of all, let’s insert a ’file’ node to the new workflow. If non of the operators is selected in the main window the middle click in the scenario builder inserts the ’file’ node 14. Open options dialog for ’file’ node. If ProStack modules for OMERO are properly installed the dialog contains the button ’Network’ 15 in the bottom-left corner. Press this button to connect to OMERO server, type the hostname and port number together with user’s credentials 16. Navigate to the needed image in the browser and press ’Select’ 17.
Insert omero_exporter module to the scenario and open the options dialog 18. The hostname and the port number are to be provided together with user’s credentials. The maximum projection is computed by the ’max3d’ operator that is to be inserted next.
The module omero_importer is used to insert the resulting image into the dataset 19.