Spots selection

One of the main features of the ST Viewer is the possibility to select spots and store the selections to later do analysis with them. In order to be able to select a spot if must be visible in the tissue. Once a selection is made and stored all the genes present in the spots will be included. There are two different ways to select:

1. Manual selection

   • Rubber-band selection
     • First enable the selection mode by clicking on ()
     • Now you can use the left click (keep it pressed and then release) to create rectangles where all the spots inside it will be selected
   • Lasso selection
     • Enable the lasso selection mode by clicking ()
     • Now you can use the left click (keep it pressed and then release) to create any shape where all the spots inside it will be selected

2. Selection trough spots classification window

   • Click on the spots classification button () in the main view
   • Perform the spot classification with the desired settings
   • Use the scatter plot to select spots with a lasso selection tool (using the mouse's right click)

An important feature is that selections made can be aggregated and/or subtracted. To aggregate selection simply keep CMD + SHIFT pressed and to subtract selections keep CMD + SHIFT + CTRL pressed.

Once a selection is made you can store it (Selections view) clicking on () button in the main view.

Here is an example of how it would look when some spots have been selected:

Selected spots are shaped as boxes and reduced in size in order to be able to distinguish them from non selected ones.