Particle Selection from a Single Image

Access: CP::Particle::Single Image (Tab)




PARTICLE supports both computational and manual particle selection from micrographs.  While computational screening has the potential for significantly higher throughput, manual selection can often achieve improved accuracy because of human's still superior ability in pattern recognition (which, unfortunately, could introduce subjective bias too).  In PARTICLE, these two functions can operate collaboratively to identify particles with both quantity and quality.  As always, visual inspection of the result is recommended because the accuracy of a computational screening highly dependents on the image quality (contrast, SNR, etc.).

EM micrographs, and cryo-EM in particular, often have low SNR.  Consequently, the result of particle screening will likely contain false-positives.  By design, PARTICLE integrates the process of particle selection, alignment and classification to identify "good" particles.  Thus, the program is able to tolerate substantial amount of false-positives in the initial particle dataset, thereby relaxing the quality requirement at the stage of particle screening (and reducing the number of false-negatives as well).  Note that a large number of false-positives will also unnecessarily increase the overall data volume.  Therefore the investigator's discretion for an appropriate balance remains indispensable.


Computational Screening

PARTICLE applies a template-matching algorithm in computational particle screening, which requires that a set of parameters to be defined in the Particle Parameter group:

In addition, a set of particle templates should be defined in the Reference Image group:

Once the particle parameters and the reference stack have been set, the Screen button will initiate the calculation of a scoring map.  Upon completion, candidate particles will be marked according to the screening threshold.  The threshold can be modified afterwards, and the screening result will be updated dynamically via the Screen button.  The number of identified particles is displayed at both the Particle Parameter::Count and the DP::DataInfo::Particles value-boxes.


Manual Annotation

The function of manual annotation is facilitated by the following keyboard/mouse combination in the DP::MainDisplay window:

When CP::Particle is activated, a toolbox becomes accessible in DP::ToolBar, which contains toggle buttons (on/off) that control data visualization in particle annotation and inspection:


Particle Stack

The coordinates of selected particles in a micrograph can be saved into a data file, and the particle images can be grouped into a stack.  These functions can be accessed from the buttons located at the bottom of the page:


CMX-Mode

To run computational particle screening in the CMX-mode, the CMX parameter setup can be exported and imported via the buttons on top of the Particle Parameter group: