Volume Viewer in OMERO.web
Open Astex Viewer
From the 4.3.2 release of OMERO, the web client includes the Open Astex Viewer for viewing images as volumes. Modifications have been made to the viewer by the EMDataBank.org team, including changes improve memory use (suitable for web browser).
Due to the memory requirements of displaying large volumes, Volume viewing is only supported for images of a limited size. Currently this is set to a volume equivalent of 120 x 120 x 120 pixels. However, if your OMERO.web server has the Python SciPy library installed, then this allows viewing of larger images by scaling down. The size limit is then due to performance of accessing all the pixel data in the volume. This is currently set at 300 x 300 x 300 but can be configured as described on this page. When viewing images larger than 120 x 120 x 120, we provide the option of viewing the images in their original size, up to 160 x 160 x 160.
By default, Open Astex Viewer will display "8 bit" images, compressing larger pixel types to save on data transfer to the client. We have found that in most cases this does not affect the quality of the volume rendering. However, we also provide the option to view the 'raw' data, for images that use floating point pixel data.
Other features/limitations in the 4.3.2 release:
- Contour slider, for adjusting the contour level of the volume. The starting point for this slider may not correspond exactly to the initial rendering in the viewer.
- Open Astex Viewer only displays a single channel/volume for any image. This will be the first Channel. It will also display only the first Time-point of any time-lapse image.
