View images in OMERO.imageviewer

OMERO.imageviewer is a basic 2D viewer which can open and browse multi-t, multi-z and multi-channel images and allows to show Regions of Interest (ROIs) and adjust rendering details including displaying histogram.

Description

We will show here:

  • How to open multidimensional images in OMERO.imageviewer

  • How to change rendering settings in OMERO.imageviewer and scroll through z and t

  • How to use the Histogram feature

  • How to zoom the image and see the scale bar

  • How to see a maximum intensity Projection

Resources

Example image used can be found under Project omero-training in Group Training_Jan_2025

Note: Only some of the images in this dataset are z-stacks, for example

  • Dataset siRNAi-HeLa, image IN_03.r3d_D3D.dv

  1. Double-click on an Image thumbnail, or click the icon next to the Full Viewer viewerlisticon button in the right-hand pane to open an Image in a larger viewer called OMERO.imageviewer. It is a Web app developed and released independently from the webclient. The OMERO.web framework can be extended with multiple apps to view data in different ways.

  2. Zoom in and out of the image by using the + and - buttons in top-left corner or by scrolling the mousewheel.

  3. We can adjust the rendering settings and scroll through Z or T.

    ../../_images/imageviewer.png

  4. On the left panel, you can also show the intensity of the channel as Grayscale by checking the checkbox.

  5. Still staying in the left panel, click on the Edit link next to the Channels word near the middle. A rendering panel will appear. renderingdetails

  6. Click on the histogram checkbox on the floating Rendering Details panel. A histogram of the first channel will appear. Note that when you move the rendering settings sliders beneath the histogram, the histogram updates to showing the channel you just manipulated. histogram

  7. Click on the Copy on the right hand panel under Rendering Details on on top of the floating window, you can save the settings of your rendering settings and you can open another image and click on Paste to set the image with the same rendering setting. You can also save the settings by clicking on the Save to save the setting.

  8. You can switch on or **off* on each of the channels on the

  9. Click on the Max Intensity on the top right panel to get the Maximum Intensity Projection of a z-stack.

  10. Click on Image Information on the righthand panel, a floating window of Image Information will appear.