Modular software platform for low‐dose electron microscopy and tomography

Abstract

SummaryTransmission electron microscopy imaging protocols required by structural scientists vary widely and can be laborious without tailor-made applications. We present here the JEOL AUTOMATED MICROSCOPY EXPERT SYSTEM (JAMES) API INTEGRATOR, a programming library for computer control of transmission electron microscopy operations and equipment. JAMES has been implemented on JEOL microscopes with Gatan CCDs but is designed to be modular so it can be adapted to run on different microscopes and detectors. We have used the JAMES API INTEGRATOR to develop two applications for lowdose digital imaging: JAMES imaging application and the MR T tomographic imaging application. Both applications have been widely used within our NCRR-supported Center for routine data collection and are now made available for public download.

Computer controlled cryo-electron microscopy – TOM2 a software package for high-throughput applications

“…Others offer in addition graphical user interfaces (GUIs) that facilitate their use. While the latter provide a higher level of automation they are generally dedicated to one specific task, such as tomography (Braunfeld et al, 1994;Kisseberth et al, 1997;Marsh et al, 2007;Mastronarde, 2003Mastronarde, , 2005Rath et al, 1997;Zheng et al, 2004Zheng et al, , 2009Zheng et al, , 2007b, random conical tilt acquisition (Yoshioka et al, 2007;Zheng et al, 2007a), single particle acquisition (Carragher et al, 2000;Lei and Frank, 2005;Stagg et al, 2006;Zhang et al, 2009Zhang et al, , 2001Zhang et al, , 2003 or electron crystallography (Cheng et al, 2007;Coudray et al, 2011;Hu et al, 2010;Oostergetel et al, 1998). Some acquisition packages have been adopted to perform multiple acquisition tasks such as UCSF Tomo and Leginon (Suloway et al, 2009), or the TOM Toolbox (Nickell et al, 2007).…”

A Script-Assisted Microscopy (SAM) package to improve data acquisition rates on FEI Tecnai electron microscopes equipped with Gatan CCD cameras

“…A modular software platform called JAMES has recently been developed for JEOL microscopes with Gatan CCD cameras (Marsh et al, 2007). JAMES provides a single interface to both a JEOL microscope and a Gatan CCD camera and allows the skilled microscopist to remain in control of most decisions during a microscopy session.…”

An approach to automated acquisition of cryoEM images from lacey carbon grids

“…This is done by linking together existing implementations of functionality in Leginon - called “nodes” - or by developing new nodes (in the source language of Leginon, Python). Various other packages have been developed for automated data collection including JAMES (Marsh et al, 2007), JADAS (Zhang et al, 2009), AutoEM (Zhang et al, 2001; Zhang et al, 2003) and AutoEMation (Lei and Frank, 2005). Recently, the SAM software was developed for semi-automated image collection and is suitable for use with lacey grids (Shi et al, 2008).…”