The graphical annotation window consists of:
First of all, note the functionality: while you are in the graphics tool mode you will be creating new graphics elements. Therefore the first thing you do is click on "Edit tool" on the top left Tool list. While in edit mode you can click on graphics elements on the screen to select them. If you click inside the circle and while holding the left button move the mouse you will move the circle. If you click on the circle circumference and move the mouse while holding the button you will resize the circle.
If you click right button, you will see the pop-up menu where you can select properties and change color, thickness, line style, name and add description.
While in graphical annotation you can press button "save" in the lower right corner and that will save the annotations into the file.
We do have a way of storing annotations. They don't go into the arbitrary XML file but rather in a particular one. The annotations, graphical and non graphical are stored into the file called .bix with the same name as image file. e.g. for the image my_image.tif the metadata will be stored in my_image.tif.bix
The BIX file is an XML file where you will find all the annotations and inside the value of <item type="graphics" >, in this case the XML annotation is stored into the CDATA field. The default file is a legacy file and we have the new way of storing the annotations with the same notation as our data-base XMl file is. This is configurable in the ini file. Although we do still maintain compatibility for the textual annotations.
All the graphical objects do live in the 5D space, although we do not account for channel currently the T and Z dimensions are used. By default all graphical objects live in their current plane. This means that if you open a multi-page tiff and go to plane 3 and put a point and a circle on it they will only live and be visible on plane 3. (There's a button to project all annotations on current plane though: "Show on all pages"). Once created you can change the plane the element lives on by going to it's properties and changing "Page", where you can set it to "All" as well. It's possible to make a type with default behavior, e.g. the type "Cell centroid" is specifically defaulted to live only on the current plane. But it is possible to create another type that would live on all planes by default.
There's a catch though: If the TIFF file does not have any meta-data to what the planes are it will use the default axis, which is configurable via the template. Actually we have configured the default axis at T for microtubule templates and Z for retina.