ArbitrEM | SerialEM scripts

ArbitrEM is a Python library typically used in Telecommunications, Media, Advertising, Marketing applications. ArbitrEM has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However ArbitrEM build file is not available. You can download it from GitHub.

The ArbitrEM workflow enables the user to collect targeted micrograph exposure movies. To allow this, foil-holes or regions of lacey specimen grids must be tracked during each of two the phases of data-collection: low-magnification view-map acquisition for targeting (the AcquireHoleViewMaps.txt or AcquireLaceyViewMaps.txt scripts), and high-magnification view-map tracking for data-acquisition, by the ArbitrEM.txt script), typically with a dose per exposure of 0.02 - 0.04 e-/Å2, during which up to 10 neighbouring holes may also be exposed depending on the specimen-foil geometry, and as a consequence, the total number of exposures must be kept to a minimum to preserve high-resolution information. On a Titan Krios a targeting accuracy of up to ± 30 nm is possible when using beam-image shift displacements of up to 2.5 µm. Accurate targeting is achieved by taking into account the offset of the specimen stage re-alignment, implying that the region does not need to be tracked with high accuracy. The workflow would typically involve microscope setup/specimen grid identification in the morning, with view-map acquisition until mid-afternoon (at a rate of ~200 per hour). At present, target selection is performed at the microsope within SerialEM (although a 'dummy' SerialEM installation can be setup at an offline Windows terminal). Movie acquisition rates are typically between 80-100 micrographs per hour when using the Gatan K2 Summit when acquiring on average two movies per view-map.