Main View

The main view (after having opened a dataset) should look like this:

There you can see on the left the "Genes" (1), "Clusters" (2) and "Spots" (3) panels, on the top the "tool bar" (4) with different buttons and in the center the "main view" (where the tissue image and the data is shown).

No data is being shown in this example (only the tissue image).

You can zoom in/out the main view with the mouse wheel and you can also also pan the main view by pressing the left click of the mouse.

The Genes, "Clusters" and Spots panels are dockable which means that they can be docked in/out and also hidden. You can also show/hide them using the tab "Views".

The main tool bar contains most of the functions available:

1. Zoom in the main view
2. Zoom out the main view
3. Rotate the main view 45 degrees to the right (disabled in 3D mode)
4. Rotate the main view 45 degrees to the left (disabled in 3D mode)
5. Invert the main view (disabled in 3D mode)
6. Show the QC stats window (disabled in 3D mode)
7. Show the Spot clustering window (disabled in 3D mode)
8. Rubber band selection mode (disabled in 3D mode)
9. Lasso selection mode (disabled in 3D mode)
10. Create and store a selection (disabled in 3D mode)
11. Select spots by gene names (disabled in 3D mode)
12. Save the main view to an image file
13. Print the main view
14. Load a list of spot colours (tab delimited file, 1st column the spot and 2nd column the colour as an integer value)
15. Load a list of gene colours (tab delimited file, 1st column the gene and 2nd column the colour as an integer value)
16. Show/hide the visual settings panel