6 Getting Data Out

OMERO.insight contains functionality to export images out of the OMERO system. This functionality can be extended using the scripting service.

6.1 Export to OME-TIFF

The OMERO.insight client allows exporting of full image stack and associated metadata to the OME-TIFF file format. This feature is available for all images on the OMERO server. First start by selecting a single image to export as shown below.

In the metadata browser panel found on the right hand side, locate the
icon.
Pressing this icon will bring up an Export dialogue box that will ask you to specify browse to a location you wish to save the image to.

Exercise 1

• Export one of your images as an OME-TIFF to your desktop.

• Open the OME-TIFF image with imageJ.

6.2 Save a rendering

Launch the image viewer by double clicking on an image in the workspace. This will bring up the image viewer as shown below.

In the image viewer there is a
icon which allows you to save the rendering to disk as an image file. Images can be saved for the Image, Split and Projection view modes.

It is also possible to 'Batch Export' rendered planes from multiple images at once using the "Batch Image Export" script. See the "Scripts" training section. Exercise 3

• Save to your desktop a PNG file of one of the Z sections of you image.
• Save a split view z section as a TIFF file.

6.3 Export a report

By selecting a dataset, it is possible to generate a report about this dataset. This exports a summary of all the Tags on the images in this dataset, as well as image thumbnails. Select a dataset from the hierarchy as shown below:

You will notice in the workspace toolbar the icon. Clicking this will bring up the Create a report dialogue box, which will ask you to browse to a location on your hard drive to save an Excel spreadsheet.
A spreadsheet will be created to generate a list of all the image names and the image ids, as shown below:

• Select a dataset and save the report to your desktop.
• Open the saved report in Excel to view the report contents.

6.4 Export Thumbnails

In a similar manner to the dataset report it is also possible to save all image names and thumbnails to an Excel spreadsheet using the icon.

• Select a dataset and export the thumbnails to your desktop.
• Open the saved report in Excel to view the contents.

6.5 Publishing Options

In the metadata browser panel found on the right hand side, locate the icon. Pressing this icon will bring up the publishing tools as shown below.

The publishing tools allow you to export images as figures, based on their annotations, metadata, ROIs etc. All figures are saved as attachments to the appropriate Project, Dataset or Image, and are also available to download. A figure legend is generated for each figure (downloaded as text file) which contains additional details for each image, such as name, ID, scale bar size, rendering settings, projected planes, pixel size, etc.

6.5.1 Make Movie...

This creates a movie for your image. You are able to specify the Z and T ranges of frames to use. Select a scale bar to be displayed and if labels should be shown.

6.5.2 Split View Figure...

Choose one or more images to be arranged in a split-view with one image per row. When making the image you can decide which channels should be shown as split panes and which are in the merged image. You can also choose names for each channel (or use existing names) and choose whether you want the split channels to be coloured or greyscale. Images can be labeled with their name, the name of their dataset(s) or associated tags.

6.5.3 ROI Split Figure...

If a rectangle ROI has previously been defined for an image (or images), then this figure will display the ROI as a larger panel to the right of the main image, zoomed by a chosen factor. The zoomed ROI will be split into selected channels, as for the split-view figure. Images can be labeled with their name, the name of their dataset(s) or associated tags.

6.5.4 Thumbnail Figure...

This creates a figure of thumbnails, either using the currently selected images or all the images within a dataset. The date range of the images is displayed on the figure, and it is also possible to choose a list of tags to sort the images by. If an image is tagged by multiple tags, it will appear more than once in the figure.

• Try exporting one of each of these publishing figures