emScope: A Tool Kit for Control and Automation of a Remote Electron Microscope

ANIMATED-TEM: a toolbox for electron microscope automation based on image analysis

“…The first software tools for the control in TEM have been devised for the automation of repetitive data acquisition tasks by executing scripts [7][8][9] and for creating dedicated interfaces for specific techniques like tomography [10,11]. Image processing techniques have first been used to design autotuning methods for accurately setting astigmatism, focus, and alignment of the microscope.…”

“…In most applications, the multi-scale approaches are used to select, among all edges detected with precision using fine scales, the more interesting edges at coarser scales [9]. In this work, a different property is used: the coarser scales increase the probability of identifying the edge transition in the noise.…”

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).…”

Leginon: a system for fully automated acquisition of 1000 electron micrographs a day

“…The size and orientation of the grid squares is determined from an initial calibration which takes only a few minutes to complete. This procedure can also be used as a stand alone application to automatically acquire low magnification preview images of an entire grid [7].…”

“…4 and it consists of the following layers: EmScope Control Server: A multi-layered software library for portable and extensible control and acquisition in a distributed software environment [7]. A server has been developed using this library that provides distributed control of all functions on the microscope and camera.…”