Description:
The Clicker module is used to create motive-lists (also abbreviated as motl), as defined in the EM-package of Reiner Hegerl,
Martinsried, Germany (Hegerl, R. (1996). The EM Program Package: A Platform for Image Processing in Biological Electron Microscopy,
J. Struct. Biol. 116: 30-34). The motive-list is a two-dimensional
matrix with a collection of all necessary information defining all the parameters of a sub-tomogram (i.e. location, translation,
rotation, class, etc. ).
The structure of the motive-list has dimension (20,NPARTICLES) and is as follows:
| column |
|
| 1 |
Cross-Correlation Coefficient |
| 2 |
x-coordinate in full tomogram |
| 3 |
y-coordinate in full tomogram |
| 4 |
peak number |
| 5 |
not occupied - e.g. use for # of tomogram of extracted particles |
| 8 |
x-coordinate in full tomogram |
| 9 |
y-coordinate in full tomogram |
| 10 |
z-coordinate in full tomogram |
| 11 |
x-shift in subvolume (AFTER rotation) |
| 12 |
y-shift in subvolume (AFTER rotation) |
| 13 |
z-shift in subvolume (AFTER rotation) |
| 14 |
x-shift in subvolume (BEFORE rotation) |
| 15 |
y-shift in subvolume (BEFORE rotation) |
| 16 |
z-shift in subvolume (BEFORE rotation) |
| 17 |
Phi |
| 18 |
Psi |
| 19 |
Theta |
| 20 |
class no |
An arbitrary amount of 3D coordinates can be selected, on an Orthoslice, Isosurface or Surface as used in
Amira, by clicking the according coordinates with the arrow mouse. Selected coordinates are visualized by spheres with a definable radius, in order to (a) visualize the selected positions
and (b) avoid selecting the same position more than once. Furthermore the module provides the possibility to load an
existing motive-list, visualize the particles as spheres and add new or remove existing positions.
Alternatively, the Clicker module provides the possibility to save the selected positions into a STAR file and load an existing STAR file to visualize the particles. To use the possibilities of STAR files the given filenames have to have the extension .star.
When loading STAR files, the module will search for the appropriate data block in the file (it will search for a data block where the data item "3D_reconstruction.file_name" is equal to the connected data file in Amira) to visualize the particles. If it does not find an appropriate data block, it will visualize the particles from the first data block.
The structure of a STAR file should at least contain the following data items:
| data_ |
|
|
|
| _{file extension}.3D_reconstruction.id |
{id} |
| _{file extension}.3D_reconstruction.file_name |
{filename} |
| _{file extension}.3D_reconstruction_select |
1 |
| _{file extension}.3D_reconstruction_voxel_size |
{voxel sixe} |
|
|
| loop_ |
|
| _particle.id |
|
| _particle.group_id |
|
| _particle.magnification |
|
| _particle.x |
|
| _particle.y |
|
| _particle.z |
|
| _particle.origin_x |
|
| _particle.origin_y |
|
| _particle.origin_z |
|
| _particle.view_x |
|
| _particle.view_y |
|
| _particle.view_z |
|
| _particle.view_angle |
|
| _particle.fom |
|
| _particle.select |
|
| {List of particle data} |
|
When saving STAR files, the module provides two possibilities:
- If the STAR file with the given filename does not exists, the module creates a new file with one data block with the appropriate particle data.
- If the STAR file with the given filename exists, the module will search for the appropriate data block in the file (it will search for a data block where the data item "3D_reconstruction.file_name" is equal to the connected data file in Amira). If the module finds the data block, it will update the particle data, otherwise it will append a new data block at the end of the file.
Ports:
Load an existing motl
This radio box defines whether an existing motive-list respectively STAR file should be loaded or a new one should be created. An existing motive-list respectively STAR file can be completed.
Size
This slider defines the radius of spheres localized at the coordinates of the next clicks. Already visualized spheres will only
change the radius when the Apply button is pressed.
Color
This radio box defines whether the color of the spheres is derived from the z value of the clicked coordinates
or the color is chosen from the port Colormap. To change the color of already visualized spheres the Apply
button has to be pressed.
Colormap
This colormap defines the color of the spheres.
Add or remove sphere
This radio box defines whether a new sphere will be added with the next click, or an existing sphere will be removed. When the port
is set to idle nothing will happen when a point is clicked.
Filename for saving motl
This file chooser defines the path and the filename of the created motive-list respectively STAR file.
Filename for loading motl
This file chooser defines the path and the filename of an existing motive-list respectively STAR file for loading.
The port is only visible when the port Load_an_existing_motl is set to yes.
Save motl
When this button is pressed the motive-list respectively STAR file will be saved into the filename.
| 
