To activate filament picking, select the "Micrograph/Pick filament" menu item or the filament tool (linear linked nodes icon). A "Filament" menu will appear and a new window will open with buttons to manage filament picking. The filament is picked as nodes connected with a spline, defining the center of the filament.


Mouse controls for filament picking

Clicking the left mouse button in an empty region on the image creates a new node. The linkage of the new node depends on the previously selected node. Clicking the left button inside a node selects it and allows that node to be dragged.

To delete a node, hold down the shift key and click the left button inside the node.

The node radius can be changed in the "Node radius" entry box. This parameter determines the circle radius. Clicking inside this radius selects the node.

Clicking the right mouse button or Ctrl-left mouse button in an empty region on the image creates a new filament.

The profiles plot shows the cross section at the current node (red) and the average cross section over all the nodes (blue). This can be used to center the node on the filament

Extracting the filaments

The "Box width" entry determines the width of the filament image in pixels that will be extracted.

The filament image is extracted by choosing the menu item "Filament/Extract filament". A dialog box requesting a file name for the extracted filament will come up.

Saving and reading curve coordinates

The filament node coordinates can be saved in a STAR file with the main menu "Micrograph" option "Writing parameters" and read back with "Read parameters". This STAR file can be used for extracting the filament images from the micrographs and further image processing.