Points

Annotate Points

napari-tomoslice annotate \
--tomogram-directory tomograms/ \
--annotation-directory tomograms/annotations/ \
--mode points

Load a tomogram using the tomogram browser on the right panel
Annotate points:
- 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 points
Save point annotations with the 'save annotation' button on the right panel

Dipole annotation

Example point annotation STAR file

TS_01_points.star

data_points

loop_
_x #1
_y #2
_z #3
678.774568      341.384876      66.419179
639.793559      352.615130      66.419179
632.822507      398.760556      66.419179
639.420122      463.065457      66.419179
494.201621      365.134786      66.419179
503.348605      477.571296      66.419179
461.693747      477.486717      66.419179
457.720446      459.715509      66.419179
436.793306      478.880565      66.419179
...

Generate Poses from Point Annotations

napari-tomoslice generate-poses points \
--annotations-directory tomograms/annotations/ \
--output-star-file tomograms/points.star

Example poses STAR file for point annotation

points.star

data_

loop_
_x #1
_y #2
_z #3
_tilt_series_id #4
678.774568      341.384876      66.419179       TS_01
694.346706      407.600310      66.419179       TS_01
704.173561      318.692324      66.419179       TS_01
710.924732      241.589390      66.419179       TS_01
713.456050      367.965992      66.419179       TS_01
780.956540      411.036262      66.419179       TS_01
742.811183      417.607369      66.419179       TS_01
633.147579      523.881512      66.419179       TS_01
599.696447      589.845587      66.419179       TS_01
606.133068      632.562486      66.419179       TS_01
...

Convert Poses into Relion 5 STAR files

napari-tomoslice convert-poses \
--input-file tomograms/points.star \
--output-type relion5 \
--output-file tomograms/points-relion.star

Example Relion 5 STAR file for point annotation

points-relion.star

data_

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnTomoName  #4
678.774568      341.384876      66.419179       TS_01
694.346706      407.600310      66.419179       TS_01
704.173561      318.692324      66.419179       TS_01
710.924732      241.589390      66.419179       TS_01
713.456050      367.965992      66.419179       TS_01
780.956540      411.036262      66.419179       TS_01
742.811183      417.607369      66.419179       TS_01
633.147579      523.881512      66.419179       TS_01
599.696447      589.845587      66.419179       TS_01
606.133068      632.562486      66.419179       TS_01
...