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Scipion GUI

This page aims to introduce you in the usage of Scipion GUI. To start image processing in Scipion we need to run scipion from the command line. At first projects manager is displayed and we can create a new project or select one previously registered (Fig. 1). For this tutorial we registered projects TestSpiderWorkflow and TestXmippWorkflow for illustrative purposes (running scipion tests tests.em.workflows.test_workflow_spiderMDA and pyworkflow.tests.em.workflows.test_workflow_xmipp).

Create a new project

Figure 1. Create a new project

Spider Workflow

If we open TestSpiderWorkflow project GUI is loaded(Fig 2). To the left different reconstruction tasks related to Single Particle Analysis (SPA) are listed. The tree menu is loaded from a configuration file where protocols are grouped according to base classes, e.g.: Micrographs Preprocess category displays ProtPreprocessMicrographs protocols. A protocol is a processing task that involves the execution of several steps and can be associated to different workflows, e.g.: SPA or Random Conical Tilt (RCT).

To the right the sequence of protocols executed by the user and its state (running, finished, aborted) is listed. We can visualize it using list or tree views. Starting from Scipion version 1.1 it is possible to create labels associated with different protocols. You can find more details about labels here. Also we can edit or copy a protocol (to rerun it), delete it, see steps or access execution database.

Bottom right panel displays information for the selected run, such as inputs and outputs, execution logs or documentation - also provides Analyze Results button to visualize outputs.

Project GUI in Protocols Mode

Figure 2. Project GUI in Protocols Mode

If we switch to Data mode (top right), then left panel displays EM objects registered for each type and right panel displays project data tree, with protocol output objects as nodes and edges towards objects used as input. Bottom right panel displays information for the selected item, that can be opened using double click. This mode allows us to track image processing emphasizing on data handling.

Project GUI in Data Mode

Figure 3. Project GUI in Data Mode

TestSpiderWorkflow project imports a set of particles, preprocess and aligns them to finally use it as input for different 2D classification algorithms. If we open filter particles protocol (using edit) the following form is displayed:

Filter Particles Protocol Form

Figure 4. Filter Particles Protocol Form

Protocol provides cite references and help util to introduce user on the subject (Fig. 4-5). Form possess two sections: Run and Input. Run section is common to all protocols and allows the user to configure run label and comments (to personalize runs, Fig. 4); execution mode (restart or resume), host, queue and threads or MPI. Many image processing tasks are computer expensive so they need to be run on specific hosts, using queue system and parallel processing. Parallelization can be supported by underneath algorithm or enabled for protocols with independent steps.

Input section allows to specify input parameters for the task, like input particles or filter type. A brief description is provided for all of them (using help button) and for some a Search GUI to select input object (Fig. 6) or a wizard GUI (through eye button). Parameters are showed considering expert level selected (Normal, Advanced or Expert).

Protocol Cite

Figure 5. Protocol Cite

Protocol Help

Figure 6. Protocol Help

List of SetOfParticles objects registered

Figure 7. List of SetOfParticles objects registered

We can visualize filtered particles using “Analyze Results” (Fig. 7). ShowJ viewer is the default viewer for most of Scipion objects, like images, volumes, sets of images, classes, etc. It can display data in gallery and table modes and navigate trough different blocks of data. Also load single images, create subsets, etc. See ShowJ for more detail. In this project we use it to refine output from a 2D classification algorithm.

ShowJ displaying filtered particles

Figure 8. ShowJ displaying filtered particles

If we select 2D classification protocol spider-classify kmeans and open output classes, we can see representative particle for each class (Fig. 8). Third and fourth items seemed very similar so we can disable fourth item and create a subset containing only remaining classes. This operation registers a subset protocol with this classes as input and the set of classes with enabled items as output.

ShowJ displaying a SetOfClasses

Figure 9. ShowJ displaying a SetOfClasses

Xmipp Workflow

If you open TestXmippWorkflow the following project GUI is displayed (Fig. 10):

TestXmippWorkflow Project GUI

Figure 10. TestXmippWorkflow Project GUI

This project imports a set of micrographs (eg: Fig. 10), reduce its image size using downsample and estimates their CTF. Then, picks particles from micrographs and extracts particles to use it as input for alignment and classification algorithms like cl2d, ml2d, kendersom or rotational spectra. We use it to illustrate CTF and particle picking GUIs.

ShowJ displaying input micrograph with "gaussian blur" filter applied

Figure 11. ShowJ displaying input micrograph with “gaussian blur” filter applied

ShowJ GUI for single images is displayed above (see Showj)

Screen micrographs produces this output:

CTF Recalculate Wizard

Figure 12. CTF Recalculate Wizard

We can use CTF wizard to redefine input parameters to recalculate CTF on specific micrographs. Recalculate CTFs will register a new protocol that receives this SetOfCTF as input and creates an output set with CTFs updated.

Particle picking can be done in Scipion using Xmipp, Eman, Bsoft, etc. In this tutorial we chose Xmipp Particle Picker, see Fig. 12.

Xmipp Particle Picker GUI

Figure 13. Xmipp Particle Picker GUI

The Xmipp picker allows us to iterate over the micrographs to pick particles, see Picker. After we have done some manual/supervised picking and feel confident with the results we register output coordinates into Scipion using Add Coordinates button.