.. figure:: /docs/images/scipion_logo.gif
   :width: 250
   :alt: scipion logo

.. _tomography-tutorials:


Tomography in Scipion
---------------------
Introduction to how Scipion integration and visualization capabilities can simplify your cryo electron
tomography pipeline.

 *Guide*: :ref:`Tomography intro <tomography-intro>`

Tomogram Reconstruction
-----------------------
The main goal of this tutorial is to illustrate the combination of different tomography software
packages in the same Scipion project.

 *Guide*:
 `Tomogram Reconstruction <https://docs.google.com/document/d/1ESIGTwPyunnelq4zCVrSL1BSqn-Qpf0tCcN-vY_mCtk>`_


Manual Tomogram Reconstruction with etomo
-----------------------------------------
This tutorial shows how Scipion incorporates etomo (scipion-em-imod) and how the tomograms can be manually reconstrutedthewith it, inside a Scipion project.

 *Guide*:
 `Manual Tomogram Reconstruction <https://docs.google.com/document/d/1TvdtTAojfAwSeQMfGdkXWIWTC7vobgicbYTq4aX1-H8>`_


Tomogram reconstruction with SCIPION: from raw movies to a tomogram
-------------------------------------------------------------------
This tutorial aims to familiarize you with initial steps of cryo-electron tomogra-
phy (cryo-ET) analysis using Scipion framework.
We assume you are familiar with Scipion GUI and have some experience with
cryo-ET data processing. Here we will demonstrate the workflow starting from raw
data up to the tomogram reconstruction, highlighting the features of our software
framework. After that, you should be able to run Scipion with your own data.

 *Guide*:
 `From raw movies to a tomogram <../../_static/pdfs/Scipion_Tutorial_Tomogram_Reconstruction.pdf>`_

Tomogram Reconstruction and Local Resolution Analysis with MonoTomo
-------------------------------------------------------------------
This tutorial shows how to reconstruct a tomogram in Scipion evaluating its local resolution

 *Guide*:
 `Local Resolution of a Tomogram Reconstruction <https://docs.google.com/document/d/1GfyYaHKaKivptV9wu-nRQSRIiq9onsC-I3qAbv25YUE>`_

Picking Tutorial
-----------------
This page will present the different picking protocols and strategies available in Scipion for Tomography and the Plugins where the various programs can be found.
The tutorial will cover from the picking step to the extraction of the coordinates selected in the tomogram, including some useful tools to complement the protocols involved in the picking workflows.

 *Guide*: :ref:`Picking tutorial <tutorial-picking>`


Denoising, Membrane Segmentation and Annotation and Directional Picking
----------------------------------------------------------------------------------

This tutorial covers a part of the full data processing pipeline in cryo electron tomography, concretely from the
tomogram to the initial model generation after having picked the particles.

 *Guide*: :ref:`Denoising, Membrane Segmentation and Annotation and Directional Picking <tomosegmemtv-pyseg-workflow>`


Subtomogram Averaging Ribosome (Part I)
---------------------------------------

In this tutorial, we will describe a basic workflow that goes
from a tomogram containing purified ribosomes to a subtomogram average of the
ribosome. To achieve this task, we will import the data to Scipion and then,
perform a picking, extraction, classification and subtomogram refinement.

 *Guide*:
 `Subtomogram Averaging Ribosome <https://docs.google.com/document/d/1wH9vCDVbjlkMwGiXB3-BsKfNEr-vKgKDry8CRHch9Yk>`_


Subtomogram Averaging HIV (Part II)
------------------------------------
In this first part of the tutorial, we will follow a workflow from tomogram to
subtomogram averaging. Our objective is to reconstruct a protein of the
capsid of the HIV virus, so our particles will have to maintain the orientation
with respect to the virus internal membrane.

 *Guide*:
 `Subtomogram Averaging HIV <https://docs.google.com/document/d/1i7nzRV5NWgmw7tPfvlVcVKSkX7_YJUMUenGPZfGN8qw>`_

Subtomogram Averaging Ribosome with EMAN plugin for Scipion
-----------------------------------------------------------

This tutorial illustrates how to carry out a subtomogram averaging (STA) with a per-particle per-tilt (PPPT) approach
using EMAN plugin for Scipion combined with others

 *Guide*: :ref:`Subtomogram Averaging Ribosome with EMAN plugin for Scipion <emantomo-sta-workflow>`

Tomography in streaming
------------------------------------
This tutorial guide you in a streaming tomography acquisition using Scipion.
To achieve this goal, we will import the tilts as a movie in SPA, we will align
those with the align protocols of SPA, we will compose the tilt serie and as the
last step we will generate the tomogram. All the steps running in streaming

 *Guide*: :ref:`Tomography in streaming <tomostreaming>`