This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We have continued development and support of the IMOD software package for tomographic reconstruction and image display, modeling, and analysis. Major milestones were the first release of the eTomo graphical interface for tomogram generation (described elsewhere) and the release of fully functional versions for Microsoft Windows and Macintosh OS X operating systems. Some significant functionality was added in the past year, including a program for automatic removal of X-rays from CCD camera images, the ability to bin down images when loading them into the 3dmod display and modeling program, and other changes to facilitate working with very large data sets. We developed a new method for providing parameter input to programs, to make it easier to run them manually or from other programs such as eTomo, to allow new options to be added to programs without breaking existing code and command files, and to centralize the specification and documentation of program options. About 15 Fortran programs have been converted to the new method. There were also major improvements in documentation: a guide to 3dmod was revised and greatly expanded to provide a comprehensive introduction to the program;a guide to tomography was thoroughly revised to describe how to work through eTomo;and a tutorial for building tomograms was also released, together with a complete dual-axis data set. With the release of versions for new platforms, downloads of the software are higher than ever. For the 2 weeks after the major version release in November 2003 plus 7 weeks in February/March 2003, there were downloads from 299 distinct IP addresses, of which 49% were for Windows, 25% for Linux, 21% for Macintosh, and 5% for SGI.
| Giddings Jr, Thomas H; Morphew, Mary K; McIntosh, J Richard (2017) Preparing Fission Yeast for Electron Microscopy. Cold Spring Harb Protoc 2017: |
| Zhao, Xiaowei; Schwartz, Cindi L; Pierson, Jason et al. (2017) Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium ""Candidatus Pelagibacter ubique"". Appl Environ Microbiol 83: |
| Brown, Joanna R; Schwartz, Cindi L; Heumann, John M et al. (2016) A detailed look at the cytoskeletal architecture of the Giardia lamblia ventral disc. J Struct Biol 194:38-48 |
| Saheki, Yasunori; Bian, Xin; Schauder, Curtis M et al. (2016) Control of plasma membrane lipid homeostasis by the extended synaptotagmins. Nat Cell Biol 18:504-15 |
| Höög, Johanna L; Lacomble, Sylvain; Bouchet-Marquis, Cedric et al. (2016) 3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction. PLoS Negl Trop Dis 10:e0004312 |
| Park, J Genevieve; Palmer, Amy E (2015) Properties and use of genetically encoded FRET sensors for cytosolic and organellar Ca2+ measurements. Cold Spring Harb Protoc 2015:pdb.top066043 |
| McCoy, Kelsey M; Tubman, Emily S; Claas, Allison et al. (2015) Physical limits on kinesin-5-mediated chromosome congression in the smallest mitotic spindles. Mol Biol Cell 26:3999-4014 |
| Höög, Johanna L; Lötvall, Jan (2015) Diversity of extracellular vesicles in human ejaculates revealed by cryo-electron microscopy. J Extracell Vesicles 4:28680 |
| Marc, Robert E; Anderson, James R; Jones, Bryan W et al. (2014) The AII amacrine cell connectome: a dense network hub. Front Neural Circuits 8:104 |
| Weber, Britta; Tranfield, Erin M; Höög, Johanna L et al. (2014) Automated stitching of microtubule centerlines across serial electron tomograms. PLoS One 9:e113222 |
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