The Open Microscopy Environment

We are pleased to announce the release of OMERO.figure 1.1.0. This release adds a number of features to the editing and export of figures.

Watch a demonstration of these new features or read their description below:

Multiple page figures:

Under File > Page Setup you can choose up to 10 pages for the figure.
Pages are laid out in a grid on the canvas and image panels can be dragged across the canvas onto the chosen page.
Export will generate a multi-page PDF document or multiple TIFF images.

Crop to region or ROI:

A crop button beside the panel zoom slider launches a crop dialog.
The crop region can be manually chosen by dragging to select an area of the displayed image.
Alternatively, existing Rectangular ROIs on the image will be loaded from OMERO and can be picked as a crop region.

Set dpi of panel images:

On the ‘Info’ tab, you can set a minimum resolution for image panels when they are embedded within the PDF figure on export. For example, 300 dpi is required by many journals.
The Info tab will then display the ‘current’ dpi in the figure alongside the export dpi.
When the figure is exported as PDF, the resolution of these panels will be boosted if it is less than the chosen export dpi.
Additional pixels will be created in the image and the data resampled using a bicubic filter.

Export of figures as TIFFs:

You can now choose to export the figure as a TIFF image at 300 dpi.
This matches the submission format for many journals and allows easy embedding in presentations.
Images are resampled using a bicubic filter to match the final figure dpi.
Multi-page figures will be exported as multiple TIFFs in a zip file.
A PDF info page is also included if your export is in a zip.

Export of panel images alongside figure:

An additional export option allows the constituant images within a figure to be exported alongside the figure as TIFFs.
For each image panel, the full sized TIFF of the image is exported, as well as the cropped and rotated TIFF that is embedded within the PDF or TIFF figure.
If images are resampled to increase their dpi, they will be saved before and after resampling.
This provides greater clarity as to the processing steps used in generating the figure and the TIFF images could also be used for creating figures in other applications.

Figure legend:

Legends can be added to figures and will be included in the info PDF page when the figure is exported.
You can use Markdown syntax to add simple formatting, such as bold and italics. Other formatting is supported in the web view, but may not be displayed properly in the exported PDF info page.

Other features:

When multiple panels are selected, they can be automatically resized to “Align their Magnification” such that features appear the same size in all panels.
Labels can be added to Scalebars to indicate their length.
A color picker allows any color to be chosen for image channels and labels.
Units support: If used with OMERO 5.1, the pixel size units in imported images will be used for scale bar labels.
Unicode support: Figures can now contain special characters.
Figure export errors are now handled with an error button which displays the error in a new browser tab.

Bug fixes:

Grab the release from the OMERO.figure 1.1.0 download page.

Release of OMERO.figure 1.1.0