Dipoles
Annotate Dipoles
napari-tomoslice annotate \
--tomogram-directory tomograms/ \
--annotation-directory tomograms/annotations/ \
--mode dipoles
- Load a tomogram using the tomogram browser on the right panel
-
Annotate dipoles:
- Shift + click and drag to move the plane up/down
- Press 'x', 'y', 'z', or 'o' to reorient the plane
- Alt + click to position the center of the dipole
- Press 'v' to define the direction of the dipole vector
- Alt + click again to move/shift the dipole
- Press 'n' to start a new dipole
- To go back and change the position or direction vector of a previously added dipole:
- Select the dipole using 'Select points' from the Napari layer control panel on the left
- Alt + click to move/shift the position of the dipole
- 'v' to change the direction of the dipole
- To move the plane during/after adding dipoles:
- Select the tomogram layer from the Napari layer list control panel on the left
- Shift + click and drag to move the plane up/down
-
Save dipole annotations with the 'save annotation' button on the right panel
Example dipole annotation STAR file
data_dipoles
loop_
_x #1
_y #2
_z #3
_direction_x #4
_direction_y #5
_direction_z #6
368.092987 62.774464 47.000000 -0.491499 0.870878 0.000000
315.885254 156.151306 47.000000 -0.555069 0.831804 0.000000
263.149506 249.084579 47.000000 -0.481098 0.876667 0.000000
206.995789 347.166748 47.000000 -0.531959 0.846770 0.000000
159.092438 439.703857 47.000000 -0.523566 0.851985 0.000000
Generate Poses from Dipole Annotations
Direct Dipole
napari-tomoslice generate-poses dipoles direct \
--annotations-directory tomograms/annotations/ \
--output-star-file tomograms/direct.star
Example direct poses STAR file for dipole annotation
data_particles
loop_
_x #1
_y #2
_z #3
_rot #4
_tilt #5
_psi #6
_tilt_series_id #7
368.092987 62.774464 47.000000 -90.000000 90.000000 60.560842 TS_01
315.885254 156.151306 47.000000 -90.000000 90.000000 56.284523 TS_01
263.149506 249.084579 47.000000 -90.000000 90.000000 61.242866 TS_01
206.995789 347.166748 47.000000 -90.000000 90.000000 57.862084 TS_01
159.092438 439.703857 47.000000 -90.000000 90.000000 58.428239 TS_01
Disk Dipole
napari-tomoslice generate-poses dipoles disk \
--annotations-directory tomograms/annotations/ \
--output-star-file tomograms/disk.star \
--distance-between-particles 10 \
--disk-radius 30
Example disk poses STAR file for dipole annotation
data_particles
loop_
_x #1
_y #2
_z #3
_rot #4
_tilt #5
_psi #6
_tilt_series_id #7
368.092987 62.774464 77.000000 -90.000000 90.000000 60.560842 TS_01
355.029815 55.401978 68.339746 -90.000000 90.000000 60.560842 TS_01
363.738596 60.316969 68.339746 -90.000000 90.000000 60.560842 TS_01
372.447378 65.231959 68.339746 -90.000000 90.000000 60.560842 TS_01
381.156159 70.146950 68.339746 -90.000000 90.000000 60.560842 TS_01
350.675425 52.944483 59.679492 -90.000000 90.000000 60.560842 TS_01
359.384206 57.859473 59.679492 -90.000000 90.000000 60.560842 TS_01
368.092987 62.774464 59.679492 -90.000000 90.000000 60.560842 TS_01
376.801768 67.689455 59.679492 -90.000000 90.000000 60.560842 TS_01
...
Convert Poses into Relion 5 STAR files
napari-tomoslice convert-poses \
--input-file tomograms/disk.star \
--output-type relion5 \
--output-file tomograms/disk-relion.star
Example Relion 5 STAR file for dipole annotation
data_particles
loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_rlnTomoName #7
368.092987 62.774464 77.000000 -90.000000 90.000000 60.560842 TS_01
355.029815 55.401978 68.339746 -90.000000 90.000000 60.560842 TS_01
363.738596 60.316969 68.339746 -90.000000 90.000000 60.560842 TS_01
372.447378 65.231959 68.339746 -90.000000 90.000000 60.560842 TS_01
381.156159 70.146950 68.339746 -90.000000 90.000000 60.560842 TS_01
350.675425 52.944483 59.679492 -90.000000 90.000000 60.560842 TS_01
359.384206 57.859473 59.679492 -90.000000 90.000000 60.560842 TS_01
368.092987 62.774464 59.679492 -90.000000 90.000000 60.560842 TS_01
376.801768 67.689455 59.679492 -90.000000 90.000000 60.560842 TS_01
...