4. Exclude tilt images
Warning
Napari is graphics intensive. This tool might not work over the browser. We strongly recommend using a local installation of Napari.
In this step, we exclude bad tilt images from the tilt series. This is an important step to ensure that the subsequent processing steps are not affected by poor-quality images. For this, we use the Exclude Tilt Images job in Doppio. This job is a wrapper around Napari excludetiltimages tool in RELION tomography pipeline. To run this job, go to NEW JOB tab in Doppio GUI and find the Exclude Tilt Series and choose Napari Exclude Tilt Series job.
As inputs, it requires a tilt_series.star file from either Motion correction or CTF estimation job. In this example, we use the output from the CTF estimation job, CtfFind/job003/tilt_series_ctf.star.
Choose the Number of cached tilt series to the number of tilt series you want to load in Napari. Choose the Number of MPI procs to 1 and click on RUN.
That will open Napari. You will see the images are being loaded on the right-bottom corner.
Napari viewer may not be responsive during the loading. Once all the images are loaded, you will see the tilt images in the Napari viewer.
By default, all images are included in the tilt series. You can exclude bad images by unticking the checkbox next to the image.
NAPARI IMAGE VIEWER - todo
Once all the unwanted tilt images are excluded, click on the Save Tilt Series button and move on to the next tilt series.
Finally, close the Napari viewer. The job will finish and produce an output star file at ExcludeTiltImages/job004/selected_tilt_series.star.
More details about the Napari Exclude Tilt Images tool can be found in the RELION documentation below.