Xmipp Picker

Overview

The Xmipp picker allows us to iterate over the micrographs to pick particles either manually or automatically, or visualize them (Fig. 1). It is the default viewer for Scipion coordinates. It provides different tools to make easier the picking process. At first, from the picker GUI, the active micrograph is loaded. In order to pick particles we can navigate over the micrograph using the mouse right click and zoom in/out the image using Shift + mouse scroll. After some training we can activate autopick to pick particles automatically.

Fig. 33 Fig. 1. Picker main GUI

Toolbar

From the toolbar we can select particle size, color and shapes: circle, square, center. Also to speed the picking process up we can use the tool . This tool centers particles automatically, using templates (see section Window: Particles and Templates). The button, when activated, allows the user to retain magnification and source rectangle when switching from one micrograph to another.

Menu

Import Coordinates

If we have done some picking before, we can import coordinates from previous projects. Formats supported include Eman, Relion or Xmipp (Fig. 2). Import can be done from a folder or from files. If import from folder is used, micrograph coordinates are loaded from the file name that results from adding the prefix and suffix specified to the micrograph name. If required, we can also invert X or Y axis, or apply some scale factor to coordinates.

Fig. 34 Fig. 2. Import particles dialog

Filters

To increase signal to noise ratio, micrographs are filtered using Gaussian Blur and Enhance Contrast, although different filters can be applied. Available filters include: Bandpass Filter, Anisotropic Diffusion, Invert LUT, etc. These filters are part of the ImageJ image processing software. When selected every time an image is loaded they are applied. For more advanced operations we can open ImageJ and process image manually.

Windows: Particles and Templates

Templates represent the different views of the particles available for a sample. The user must specify its number so that each template can be calculated automatically as we pick particles (using cross-correlation) (Fig. 3). They are used to center particles and to train classifier for autopicking.

Fig. 35 Fig. 3. Templates

Particles picked can be displayed and centered using particles window, shown below, since this window provides more detail.

Fig. 36 Figure 4. Particles

Help

From the help menu the user can access this url or visualize help tips.

Fig. 37 Figure 5. Help tips

Autopick

Autopick option allows us to pick particles automatically using Xmipp classifier. At first it needs to be trained providing a rectangle (detected automatically) fully picked, containing at least 15 particles. If previous micrographs have been picked they are also used for training. Once selected every time a new micrograph is loaded particles are picked automatically. Particles added or deleted after automatic picking can be used to correct classifier learning. Particles picked can be filtered using threshold and explore attributes. Threshold attribute allows us to dismiss particles based on its score. Explore attribute allows us to limit the profusion of particles automatically picked.

Output Coordinates

Finally after we have done some manual/supervised picking and feel confident with the results we can register output coordinates into Scipion using Add Coordinates button. An output set of coordinates will be created as protocol output.