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Import data into the pipeline
================================

To import data into the pipeline we use the *import* job in Doppio.
Go to :purple:`NEW JOB` tab in Doppio GUI and type "import" in the search bar. You will see two import jobs. The Import raw tilt images is the one we need as we are importing tilt series images.
Click on the **Import raw tilt images** job and you will see a new window with the job parameters.

.. image:: ../_static/images/STA/import1.png
   :alt: Example image
   :width: 60%
   :align: center

.. note::
   :class: note

   The import job parameters are the same that for Relion tomo Import job. We provide the
   job parameters that we use below for reference.
   The Relion tomo Import job allows you to import tilt series images as well as coordinates. In Doppio, we
   have two separate jobs for importing tilt series images and coordinates.

Here are the parameters used to import the tilt series:

.. image:: ../_static/images/STA/import-job-params.png
   :alt: Import Job Parameters Screenshot
   :width: 100%
   :align: center


`Relion tomo Import job documentation <https://relion.readthedocs.io/en/release-5.0/STA_tutorial/ImportTomo.html>`_ provides detailed explanation of the job parameters.

.. note::
   :class: note

   RELION expects the tilt axis angle in SerialEM convention.
   If you have other conventions (e.g., TOMO5), you may need to adjust the tilt axis angle accordingly.

Running the import job
---------------------------------
Once the parameters are set, click on the :purple:`RUN` button to start the import job. You'll see the live output in the **LOGS** tab. 


Output of the import job
---------------------------------
The output of the import job is a star file with the imported tilt series images and a set of metadata.
Once the import job is finished, you will see a new star file in ``Import/job001/tilt_series.star``. Also, Doppio
automatically opens the star file in the :purple:`RESULTS` tab.