Gregory Sharov edited this page Jun 13, 2017 · 3 revisions

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gautomatch - auto-picking

gautomatch is a GPU accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates, developed by Kai Zhang at MRC Laboratory of Molecular Biology [1]. An old version of Gautomatch was originally developed in Dr. Fei Sun’s lab 6 years ago. The basic concept was based on local cross-correlation (as described in FindEM paper) at that time. However, the concept and usage of newer version has been largely updated, which now requires only a single and simple command for accurate and 'smart' whole-dataset processing.

Brief manual describing program options and use cases can be found here.

Input parameters

To launch auto-picking you will need to select on the Input tab first the Input micrographs, that can be any SetOfMicrographs produced earlier (Fig. 1). Then you have to select Input references, that can be any SetOfAverages: either 2D class averages, calculated before, or reprojections of the known 3D structure (in this case, you have to import your reprojections as Averages). If the input micrographs and references do not have the same contrast (e.g., white particles on a dark background), select the option References have inverted contrast.

Among other options the most important one is the Threshold: cross-correlation peaks only above this value will be selected as particles. Usually, you should first run the protocol on a few micrographs with different defocus level to optimize threshold and other parameters before starting auto-picking on a whole dataset.

The protocol provides interactive wizards for choosing the particle size and for optimizing threshold value. The last one allows you to adjust threshold and immediately display the results of the picking.

Figure 1. GUI input form of the gautomatch protocol

By default, the program will guess all advanced parameters by itself, however if you want yo see all available options, choose the Advanced tab and select No for "Guess advanced parameters?" (Fig. 2). For more detailed information you can click Help button or address to the manual of the program.

Figure 2. Advanced protocol parameters

Analyzing results

When the protocol is finished you may click on the Analyze Results button, that will launch Xmipp particle picker window and display picked particles for each micrograph (Fig. 3).

Figure 3. Displaying picking results


  • [[[1]]] Zhang K. unpublished

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