@article {48715, title = {Best practices for managing large CryoEM facilities.}, journal = {Journal of Structural Biology}, volume = {199}, year = {2017}, month = {2017-08-04}, pages = {225-36}, abstract = {

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6{\textendash}7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.

}, doi = {10.1016/j.jsb.2017.07.011}, author = {Alewijnse, Bart and Ashton, Alun W and Chambers, Melissa G and Chen, Songye and Cheng, Anchi and Ebrahim, Mark and Eng, Edward T and Hagen, Wim JH and Koster, Abraham J and Lopez, Claudia S and Lukoyanova, Natalya and Ortega, Joaquin and Renault, Ludovic and Reyntjens, Steve and Rice, William J and Scapin, Giovanna and Schrijver, Raymond and Siebert, Alistair and Stagg, Scott M and et al} } @article {6320, title = {Beam-induced motion of vitrified specimen on holey carbon film.}, journal = {Journal of Structural Biology}, volume = {177}, year = {2012}, month = {2012 Mar}, pages = {630-7}, abstract = {

The contrast observed in images of frozen-hydrated biological specimens prepared for electron cryo-microscopy falls significantly short of theoretical predictions. In addition to limits imposed by the current instrumentation, it is widely acknowledged that motion of the specimen during its exposure to the electron beam leads to significant blurring in the recorded images. We have studied the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series. Our data show that the particle motion is correlated within patches of 0.3-0.5 μm, indicating that the whole ice layer is moving in a drum-like motion, with accompanying particle rotations of up to a few degrees. Support films with smaller holes, as well as lower electron dose rates tend to reduce beam-induced specimen motion, consistent with a mechanical effect. Finally, analysis of movies showing changes in the specimen during beam exposure show that the specimen moves significantly more at the start of an exposure than towards its end. We show how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Image Processing}, issn = {1095-8657}, doi = {10.1016/j.jsb.2012.02.003}, author = {Brilot, Axel F and Chen, James Z and Cheng, Anchi and Pan, Junhua and Harrison, Stephen C and Potter, Clinton S and Carragher, Bridget and Henderson, Richard and Grigorieff, Nikolaus} } @article {6319, title = {Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Nov 7}, pages = {1823-8}, abstract = {

Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.

}, keywords = {Cryoelectron Microscopy, Ice, Rotavirus}, issn = {1878-4186}, doi = {10.1016/j.str.2012.08.026}, author = {Campbell, Melody G and Cheng, Anchi and Brilot, Axel F and Moeller, Arne and Lyumkis, Dmitry and Veesler, David and Pan, Junhua and Harrison, Stephen C and Potter, Clinton S and Carragher, Bridget and Grigorieff, Nikolaus} } @article {5687, title = {An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010}, abstract = {

The analysis of microcircuitry (the connectivity at the level of individual neuronal processes and synapses), which is indispensable for our understanding of brain function, is based on serial transmission electron microscopy (TEM) or one of its modern variants. Due to technical limitations, most previous studies that used serial TEM recorded relatively small stacks of individual neurons. As a result, our knowledge of microcircuitry in any nervous system is very limited. We applied the software package TrakEM2 to reconstruct neuronal microcircuitry from TEM sections of a small brain, the early larval brain of Drosophila melanogaster. TrakEM2 enables us to embed the analysis of the TEM image volumes at the microcircuit level into a light microscopically derived neuro-anatomical framework, by registering confocal stacks containing sparsely labeled neural structures with the TEM image volume. We imaged two sets of serial TEM sections of the Drosophila first instar larval brain neuropile and one ventral nerve cord segment, and here report our first results pertaining to Drosophila brain microcircuitry. Terminal neurites fall into a small number of generic classes termed globular, varicose, axiform, and dendritiform. Globular and varicose neurites have large diameter segments that carry almost exclusively presynaptic sites. Dendritiform neurites are thin, highly branched processes that are almost exclusively postsynaptic. Due to the high branching density of dendritiform fibers and the fact that synapses are polyadic, neurites are highly interconnected even within small neuropile volumes. We describe the network motifs most frequently encountered in the Drosophila neuropile. Our study introduces an approach towards a comprehensive anatomical reconstruction of neuronal microcircuitry and delivers microcircuitry comparisons between vertebrate and insect neuropile.

}, keywords = {Animals, Brain, Computer-Assisted, Drosophila melanogaster, Electron, Humans, Image Processing, Imaging, Microscopy, Neurons, Neuropil, Software, Synapses, Three-Dimensional, Transmission}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000502}, author = {Cardona, Albert and Saalfeld, Stephan and Preibisch, Stephan and Schmid, Benjamin and Cheng, Anchi and Pulokas, Jim and Tomancak, Pavel and Hartenstein, Volker.} }