Adding entries with a "color transition" - Demexis/Starbound-ColorOptionsPicker GitHub Wiki

After uploading the JSON files, you most likely have pre-existing "colorOptions" parameter entries loaded into the "Color Transitions" list. If there were none, or you want to add other colors to the list that you will change in the future, you must select these colors in the "Original Sprite's Colors" list and click the "Add Transition" button.

You can select multiple colors by using "Shift+LMB" or "Ctrl+LMB".

There is also an alternative. You can click on a specific image pixel under the "Original Sprite" label. If you select a pixel in the image under the "Colored Sprite" label, then in addition to adding it, a window will also open for editing the selected color.