Downloads

Software

• Leginon Leginon is a system designed for automated collection of images from a transmission electron microscope. Instruments supported: FEI (Tecnai, Titan Krios, Polara), JEOL (3200, 3100, 2100, 1230), CCDs (TVIPS, Gatan, FEI), direct detectors (Gatan K2, FEI Falcon, Direct Electron DE12, DE20).
• Appion Appion is a "pipeline" for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools. The underlying packages integrated into Appion include EMAN, Spider, Frealign, Imagic, XMIPP, IMOD, ProTomo, ACE, CTFFind and CTFTilt, findEM, DogPicker, TiltPicker, RMeasure, EM-BFACTOR, and Chimera. These packages must be acknowledged by appropriate citations when used within Appion.
• ACE Automated CTF Estimation
• ACE2 A CTF Estimator (ACE) 2. ACE2 is a completely rewritten version of ACE. ACE2 adds the additional feature of robust astigmatism estimation and CTF correction with astigmatism using either a mild Weiner filter (recommended) or phase-flipping. Since ACE2 in written in objective C, it no longer requires MATLAB to work.
• DoGpicker Particle picker that uses difference of Gaussians (DoG) for picking particles
• TiltPicker A specially designed particle picker for image tilt pairs.
• Maskiton An interactive, web-based tool, for creating custom masks and performing 2D classifications on aligned single-particle EM images. Sourcecode on github.

Public Datasets

NRAMM releases a number of annotated and partially annotated datasets for public use. For example, some of the datasets are used to test new algorithms for particle picking or CTF correction. The datasets released so far are listed below with links to associated data and annotations. Please feel free to let us know via nramm at nysbc.org email if you have suggestions for making these datasets more accessible or ideas for other data that might be useful. The amount of metadata available for each data set varies. The KLH dataset is old and included here as it has been used as a standard for a large number of particle picking papers (see Zhu et al. 2004). The GroEL dataset has been used as a testbed at NRAMM for a number of studies (Stagg et al. 2006 and Stagg et al. 2008). The 50S ribosome subunit datasets were used to illustrate methods for ab initio reconstruction algorithms (Voss et al. 2010). In each case we provide links to further pages describing the datasets in more detail. Links on these pages will provide access to the native data (the images) and the means to download it, some of the metadata (e.g. the particle coordinates, defocus values etc.) and when possible links to the images via the Leginon database (Suloway et al., 2005) and the processed images via the Appion database (Lander et al., 2009). Within Leginon and Appion the data can be explored in a number of ways and various further metadata is available to explore or for download from these pages. The best way to figure out what the Appion pages can provide is to just go ahead and explore them by following the links. Public data sets: Note: Not all sets are currently available. Older sets are in the process of being retrieved from archives and will be available soon. see also Anonymous datasets

• T20S Proteasome at 2.8 Å Resolution - raw movies, frame-averaged micrographs and aligned multi-frame micrographs from Campbell et al. 2015
• Synthetic 70S Ribosome Datasets - synthetic datasets used to evaluate likelihood-based classification in Frealign from Lyumkis et al. 2013
• KLH datasets — including standard particle "bake-off" dataset from Zhu et al. 2004

• GroEL datasets — including datasets used for Stagg et al. 2006 and Stagg et al. 2008

• Ab initio model datasets — the 50S ribosomal subunit from Voss et al. 2010

• P22 datasets — mature wild type bacteriophage from Lander et al. 2006

• Lambda virion datasets — mature wild type bacteriophage lambda virions from Lander et al. 2008

• TMV datasets — unpublished Tobacco Mosaic Virus dataset

Viewing data and metadata:

• See Image_Viewers for help and instructions on using Leginon/Appion web-based image viewing pages. Note that you will need to login once as an Anonymous user before you can access the datasets. Summary information may be viewed by selecting the Summary option at the top of the viewer window which will pop up a new window. Appion processing pipeline information and all metadata may be accessed by selecting the Processing button at the top of the viewer window which will pop up a new window.