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J R Plaisier

Publications and source records attributed to J R Plaisier.

2 recordsLinked to original sources
PubMed2006

Cyclops: new modular software suite for cryo-EM.

Cyclops is a new computer program designed as a graphical front-end that allows easy control and interaction with tasks and programs for 3D reconstruction of biological complexes using cryo-electron microscopy. Cyclops' current plug-ins are designed for automated particle picking and include two new algorithms, automated carbon masking and quaternion based rotation space sampling, which are also presented here. Additional plug-ins are in the pipeline. Cyclops allows straightforward organization and visualization of all data and tasks and allows both interactive and batch-wise processing. Furthermore, it was designed for straightforward implementation in grid architectures. As a front-end to a collection of programs it provides a common interface to these programs, thus enhancing the usability of the suite and the productivity of the user.

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PubMedDate not supplied

TYSON: robust searching, sorting, and selecting of single particles in electron micrographs.

We here present TYSON, a new program for automatic and semi-automatic particle selection from electron micrographs. TYSON employs a three-step strategy of searching, sorting and selecting single particles. In the first step, TYSON finds the positions of potential particles by one of three different methods: local averaging, template matching or local variance. The practical merits and drawbacks of these methods are discussed. In the second step, these potential particles are automatically sorted according to their probability of being true positives. Many criteria are provided for this sort. In the final -interactive- step, whole categories of poorly fitting false positives can be removed with a single mouse-click. We present results obtained using cryo-EM micrographs of both spherical virus particles and asymmetric particles. The procedures are fast and use of TYSON allowed, for example, some 20,000 particles to be selected in a single working day.

Algorithms↗