.. Doppio Tomography Tutorial documentation master file, created by sphinx-quickstart on Tue Feb 18 13:09:38 2025. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Motion Correction of tilt images ================================== The tutorial data EMPIAR-10164 are not motion corrected. To carry out motion correction go to :purple:`NEW JOB` tab in Doppio GUI and type "motion" in the search bar (or you can choose the Motion Correction job from the job explorer). You will see two motion correction jobs. Choose the **RELION motion correction (Tomography)** job. This uses the RELION implementation of the UCSF MotionCor2 software for motion correction. .. note:: :class: note If you prefer to use UCSF MotionCor2, select the **RELION motion correction (MotionCor2)**. Note that MotionCor2 cannot save images in float16 yet, nor does it write out summed power spectra of movie frames for subsequent CTF estimation. Our input job parameters are shown in the image below. .. image:: ../_static/images/STA/motioncorr-job-params1.png :alt: Example image :width: 100% :align: center .. image:: ../_static/images/STA/motioncorr-job-params2.png :alt: Example image :width: 100% :align: center The job parameters are the same as for RELION motion correction job. Please refer to the RELION documentation for details on the parameters. `Relion MotionCorr job documentation `_. Running the motion correction job ---------------------------------- Once the parameters are set, click on the :purple:`RUN` button to start the job. You'll see the live output in the **LOGS** tab. Output of the motion correction job ------------------------------------ The output of the MotionCor2 job is a star file ``MotionCorr/job002/corrected_tilt_series.star``. Doppio will automatically open the corrected tilt images in the :purple:`RESULTS` tab. Example: .. image:: ../_static/images/STA/motion-cor2-output.png :alt: Example image :width: 100% :align: center