QBI Histology and Microscopy

Getting started with QBI OMERO Cloud

Omero is an Open Microscopy Environment client-server environment for imaging data storage, visualisation and analysis. It provides web based and desktop clients that allow you to access your microscopy data anytime, anywhere. A (Python) scripting service provides a means for server-side data analysis and plugins are available allowing data to be downloaded, analysed and uploaded using both ImageJ and Matlab.

Visit https://omerocloud.qbi.uq.edu.au/webclient/ and enter your UQ credentials to log in to the Omero webclient.

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After successfully logging in the webclient allows you to browse your project and data hierarchy; display images in the image viewer and allows you to launch analysis scripts. Currently the webclient does not support uploading data.

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Omero is also equipped with a desktop client (Insight) which, in addition to the functionality provided by the webclient, allows uploading of images and protocols using the Importer and Editor respectively. To launch Insight from the webclient, press Screen Shot 2014-08-08 at 11.55.50 AM on the toolbar. This will open a new window with a link for downloading the client:

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Double-clicking on any image in the webclient opens that image in the viewer:

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Clicking on the Edit hyperlink displays the rendering details which can be used to change the colour of each channel as well as the display range. The new display settings can be saved back to the server so the images appears the same next time it is opened.

The Omero scripting service can be accessed using the Screen Shot 2014-08-08 at 11.56.00 AM button.

Starting the Insight desktop client produces the following dialog:

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If the server name is set as omerocloud.qbi.uq.edu.au, enter you UQ credentials to log in to the server. Otherwise, click the spanner icon to open the Servers configuration tool. Edit the server name to read omerocloud.qbi.uq.edu.au and make sure the port is 4064. Click Apply to return to the log in dialog.

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Successfully logging in produces the Insight interface:

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Click the Screen Shot 2014-08-08 at 1.31.13 PM button to upload data to the server:

Screen Shot 2014-08-08 at 10.20.59 AMSelect images from the file browser on the left and add them to the queue on the right. When populating the queue, select which project and dataset the image(s) should be added to. If –No Project– and –New From Folder– are used, a new dataset is created in the server with the same name as the local folder in which the image resides.

Screen Shot 2014-08-08 at 10.20.44 AMClick Import to start the upload. A new tab becomes available which allows monitoring the progress of the upload:Screen Shot 2014-08-08 at 10.21.14 AM

Double click an image to open the viewer:

Screen Shot 2014-08-08 at 10.18.27 AMClick the  Screen Shot 2014-08-08 at 1.32.55 PM button on the toolbar to display the rendering settings. To change the colour of a channel click the Screen Shot 2014-08-08 at 1.39.59 PM button and select a channel to open the Colour Picker Window:

Screen Shot 2014-08-08 at 10.18.09 AMSome data analysis can be performed on the server using the scripting service. This can be accessed by clicking to the Screen Shot 2014-08-08 at 1.31.28 PM button:

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Use the Screen Shot 2014-08-08 at 1.58.13 PMbutton under General Information on the right side of the client to download data either in the original format of as OME-TIFF.

Also see http://help.openmicroscopy.org/export.html for further help in downloading your images.

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