In this document, we introduce OMERO.FPBioimage, a 3D volume viewer for OMERO.web.
We will show here:
- How to open a multi-z image in OMERO.FPBioimage
Example files used
Note: Only some of the images in this dataset are z-stacks, for example
OMERO.FPBioimage is a pip installable application for OMERO.web. Follow the steps described in https://pypi.org/project/omero-fpbioimage/ to install it and configure the OMERO.web accordingly.
Login to OMERO.web and open an image from the Dataset siRNA-HeLa with multiple Z-sections e.g. VRAQ_01.r3d_D3D.dv in a 3D viewer: OMERO.FPBioimage.
- First select the Image.
- In the Preview tab, switch off all channels except FITC and the GFP-INCENP channel.
- Save the new rendering settings.
- Use right-click menu on the image in the left panel, or the Open with… icon on top of the right-hand pane to open the image with FPBioimage.
- Click Start in the new viewer window.
- We can see that the centromeres are well aligned on the metaphase plate on the selected Image, whereas the centromeres are located in and around the spheroid on the IN_02.r3d Image for example.