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

.. _showJ:

=====
ShowJ
=====

Overview
--------

ShowJ is the default viewer for Scipion objects, like micrographs,
particles, volumes, classes, etc. Supported formats include: sqlite,
star, vol, stk, mrc, etc. It allows us to display data in gallery or
table mode |table_mode, width=20| and navigate through different
blocks of data. Single images are opened using image window. On the top of
the window we have the menu and toolbar (Fig. 1).

.. figure:: /docs/images/guis/table-mode.png
   :align: center
   :alt: Table mode.

   Fig. 1: ShowJ, Table mode


From the File menu we can display the file information (path, size, date)
and open any input file with ImageJ or Chimera if possible. We can also save
the file, or save/load a selection of Scipion objects (see Subsets).

From the display menu we can configure the columns order, render and
visibility. We can also turn on/off render and select which labels to
display with the images. We can also normalize images, flip images
vertically, etc. Developer users can configure visualization from the
command line.

Tools menu allows us to do some statistics on images, such as processing
Average (AVG) and Standard Deviation (STD), Principal Components
Analysis (PCA) or Fourier Shell Correlation (FSC). It also allows us to
find and/or replace some text |find_replace, height=20| or plot some
labels |plot_labels, height=20|.
A popup menu appears when the user right-clicks on the table displaying actions
available for the selected item. From this menu we can enable/disable items,
select a range of items, open an image, recalculate CTF, if possible, etc.
Developer users can customize this menu from the command line to add actions
related to the type of data loaded.

.. figure:: /docs/images/guis/ctf.png
   :width: 800
   :align: center
   :alt: Ctf tools.

   Fig. 2: Ctf tools


Table Mode
----------

Table mode displays visible labels of the input objects (Fig. 1) and
can display images in text or image formats. For volumes and stacks
only the central slice is shown. Input files that contain only one item are
displayed as a form. It allows us to order objects asc/desc using mouse
click on column header. Also, we can use the plot tool to display one or
several columns on a graphic using Plot, Scatter or Histogram modes (the
x column is optional).

Column properties are usually specified
from the command line (for Scipion objects). In order to modify this
configuration we can access columns window from the display menu (Fig.
3).

.. figure:: /docs/images/guis/columns.png
    :width: 500
    :align: center
    :alt: Columns Window.

    Fig. 3: Columns Window


Gallery Mode
-------------

The gallery mode displays the renderable label selected or, in the case of
volumes, volume slices, with a combo to iterate over the volumes. It is
used, for example, to visualize particles, classes and volume slices. We
can change the number of columns and rows and reslice volumes |number_of_columns, height=20|
Reslice allows us to visualize volume slices from: Front, Top, Left,
Right and Bottom perspectives.

In Scipion, after a 2D classification, particles have geometry information. We can apply
geometry or wrap these images either from the gallery or table modes:

.. figure:: /docs/images/guis/geometry.png
    :width: 700
    :align: center
    :alt: Gallery mode.

    Fig. 4: Gallery mode

Chimera projector lets us visualize and project the selected volume from different
angles (Fig. 5).

.. figure:: /docs/images/guis/chimera-viewer.png
    :width: 700
    :align: center
    :alt: Chimera viewer.

    Fig. 5: Chimera viewer

Image Window
------------

Image Window allows us to visualize single images or stacks. It is an
extension from ImageJ image processing software. We can navigate over
the image holding mouse right click and zoom in/out image using Shift +
mouse scroll (Fig. 6 and Fig. 7). Also we can apply filters on image to increase
signal to noise ratio.


.. figure:: /docs/images/guis/micrographs.png
    :width: 700
    :align: center
    :alt: Image Window.

    Fig. 6: Image Window.

.. figure:: /docs/images/guis/stack-window.png
    :width: 250
    :align: center
    :alt: Stack Window.

    Fig. 7: Stack Window

Image Filters
-------------

Available filters include Gaussian Blur, Enhance Contrast, Bandpass
Filter, Anisotropic Diffusion, Invert LUT, etc (these filters are part
of ImageJ) . For more advanced operations we can open ImageJ and process
image manually.


Mask GUI
--------

Mask GUI allows us to create a mask from an image, and register it as an
Scipion object. To draw a mask we can combine different ImageJ selection
tools and add or delete regions to selection using Shift and Alt keys
respectively. Also from the toolbar we can invert selection or smooth
the border. This tool comes handy when we need to create our own masks.

.. figure:: /docs/images/guis/design-mask.png
    :width: 700
    :align: center
    :alt: Design mask tool.

    Fig. 8: Design mask tool.

Volume Viewer
-------------

From the File menu we can use volume viewer to visualize stacks or
volumes. This plugin shows stacks as slices, projections or volumes
within a 3D-(xyz)-space:

.. figure:: /docs/images/guis/volume-viewer.png
    :width: 700
    :align: center
    :alt: Volume viewer.

    Fig. 9: Volume viewer.

Subsets
-------

Using ShowJ we can create Scipion subsets. Subsets are special protocols
that register selected/enabled items from a set as an output set. We can
create sets of the same type or sets of a different type. For example,
we can merge particles from different classes. Different selections
tools are available for the user: Select from/to, invert selection,
selection using Ctrl and Shift, etc. For large image processing tasks
that involve user interaction we can save our selections to restore them
later, since Scipion objects cannot be modified. Subsets allow us to
dismiss objects from a set without modifying the original set
(potentiating project traceability).


.. |table_mode, width=20| image:: /docs/images/guis/02.TableView.png
.. |find_replace, height=20| image:: /docs/images/guis/binocular.png
.. |plot_labels, height=20| image:: /docs/images/guis/plot.png
.. |number_of_columns, height=20| image:: /docs/images/guis/06.3DAxis.png