Grid hole picker

Dynamo includes an utility for semi-automated picking of holes on a grid. This utility can be called from SerialEM or any other data acquisition software.

An instance of the Dynamo hole picker can be invoked along with a set of .mrc files, each one containing the image a single polygon. The hole picker allows the application of a predetermined detection workflow on all the polygons, and the manual correction afterwards. It also offers the possibility of tuning the parameters in the hole detection workflow for each of the polygons separately.

The hole picker GUI

The hole picker GUI allows surfing from polygon to polygon, using the cursor keys or the << and >> pushbuttons in the GUIs.

Each time you transition the view from a polygon to another one, Dynamowill:

• the coordinates shown in screen will be saved in the .xy file corresponding to the polygon you just left.
• read the .xy coordinates of the polygon you just opened and show them on screen.

Key strokes

The pushbutton depicting a black point inside a red circle is the click switcher. When it is activated, you can use several keys to interact with the polygon shown in the main view of the Hole Clicker.

• Main click to add a point
• Secondary click to select a point
• Secondary click to move the view: zoom in and out and hand tool to shift the view
• d to delete the point closest to the cursor.
• m to move to the cursor the closest point