ShowJ
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 image::https://github.com/biocompwebs/scipion/wiki/images/gui/02.TableView.png[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).
From the File menu we can display file information (path, size, date) and open input file with ImageJ or Chimera if possible. We can also save file, or save/load selection, for Scipion objects (see Subsets).
From the display menu we can configure columns order, render and visibility. Wen can also turn on/off render and select label to render or to display with images. Also we can 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 <img src="%ATTACHURLPATH%/binocular.png" alt="find.png" height="20" /> or plot some labels <img src="%ATTACHURLPATH%/plot.png" alt="plot.png" height="20" />
Popup menu appears when the user does a right-click mouse operation 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.
<figure> <img src="%ATTACHURLPATH%/ctf.png" alt="CTF tools.png" width="800" /> <figcaption>Fig. 2. CTF tools.</figcaption> </figure>
Table mode displays visible labels for the input objects (Fig. 1) and can display images in text or image formats. Volumes and stacks display only the central slice. 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 plot tool to display one or several columns on a graphic using Plot, Scatter or Histogram modes (the x column is optional). <br/> 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> <img src="%ATTACHURLPATH%/columns.png" alt="columns.png" width="500" /> <figcaption>Fig. 3. Columns Window.</figcaption> </figure>
Gallery mode displays 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 <img src="%ATTACHURLPATH%/06.3DAxis.png" alt="06.3DAxis.png" height="20" />. Reslice allows us to visualize volume slices from: Front, Top, Left, Right and Bottom perspectives. <br/> In Scipion after a 2D classification particles have geometry information. We can apply geometry or wrap on these images either from gallery or table modes: <figure> <img src="%ATTACHURLPATH%/geometry.png" alt="geometry.png" width="700" /> <figcaption>Fig. 3. Gallery mode.</figcaption> </figure> <br/> Chimera projector let us visualize and project the selected volume at different angles (Fig. 4).
<figure> <img src="%ATTACHURLPATH%/chimera-viewer.png" alt="chimera-viewer.png" width="700" /> <figcaption>Fig. 4. Chimera viewer.</figcaption> </figure>
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). Also we can apply filters on image to increase
signal to noise ratio.
<figure> <img src="%ATTACHURLPATH%/micrographs.png" alt="Imagej Window.png" width="700" /> <figcaption>Fig. 6. Image Window.</figcaption> </figure>
<figure> <img src="%ATTACHURLPATH%/stack-window.png" alt="stack-window.png" width="300"/> <figcaption>Fig. 7. Stack Window.</figcaption> </figure>
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 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> <img src="%ATTACHURLPATH%/design-mask.png" alt="design-mask.png" width="500"/> <figcaption>Fig. 8. Design mask tool.</figcaption> </figure>
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> <img src="%ATTACHURLPATH%/volume-viewer.png" alt="volume-viewer.png" width="600" /> <figcaption>Fig. 9. Volume viewer.</figcaption> </figure>
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).