7. Picking in tomograms

Doppio supports the Napari picker implemented in RELION. This picker has individual particle picking, sphere annotation and filament picking modes. Since Napari is graphics intensive and does not scale for port forwarding, we strongly recommend to use Napari picker locally than remotely.

7.1. How to run Napari picker locally?

For this, you’ll need to install the Napari picker in your local system (aka laptop). As far as our experience goes, local installation of RELON will bring all the necessary tools into your local system.

7.2. Local installation of Napari

We’ll install Napari in a new conda environmenet in the local system.

git clone https://github.com/3dem/relion.git  # Clone RELION repository
git checkout ver5.0                           # Checkout to ver5.0 branch

conda create -n relion-picker python=3.10     # Create relion-picker conda env
conda activate relion-picker                  # activate the conda env

pip install '.[.vis]'                         # Install python modules listed in pyproject.toml
                                              # including Napari components
conda deactivate
conda activate relion-picker

7.3. Running Napari locally

Navigate to the project folder where you have copied the Tomograms folder. Then

mkdir -p Picks/job007                         # Make Picks/job007 dir for picking
relion_tomo_pick spheres --tilt-series-star-file Tomograms/job006/tomograms.star --output-directory Picks/job007

This will open Napari picker in your local system. Do the sphare annotation as explained in the Relion tutorial [link below]. Once you’ve annotated all the spheres in one tomograms click Save spheres button on the lower left and move on to next tomograms. At the end of annotation of all tomograms, close Napari-picker window. If everything is successful you’ll see TS_01_spheres.star TS_03_spheres.star files in the Picks/job007/annotations folder.

Once you have annotations, the next step is to do the sampling on the spheres to generate particle coordinates. To do that,

mkdir -p Picks/job008                         # Make Picks/job008 dir for particles
relion_tomo_get_particle_poses spheres --tilt-series-star-file Tomograms/job006/tomograms.star --annotations-directory Picks/job007/annotations --output-directory Picks/job008/ --spacing-angstroms 60

This will generate and write out particles into Picks/job008/particles.star. This is the particle.star file you’ll use for next steps.

In this exaple, we use sphere annotation of the locally installed Napari-picker, but you’ll be able to use its other picking modes as explained in the Relion tutorial below:

Relion Particle Picking job documentation.

7.4. EulerMate Particle Picking

TODO