Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both spatial and temporal resolution by preserving individual electron events. Running ReCoDe on a workstation we demonstrate on-the-fly reduction and compression of raw data streaming off a detector at 3 GB/s, for hours of uninterrupted data collection. The output was 100-fold smaller than the raw data and saved directly onto network-attached storage drives over a 10 GbE connection. We discuss calibration techniques that support electron detection and counting (e.g., estimate electron backscattering rates, false positive rates, and data compressibility), and novel data analysis methods enabled by ReCoDe (e.g., recalibration of data post acquisition, and accurate estimation of coincidence loss).
Supplementary Information are available at Bioinformatics online.
Quantitative multi-omics data are difficult to interpret and visualize due to large volume of data, complexity among data features, and heterogeneity of information represented by different omics platforms. Here, we present multiSLIDE, a web-based interactive tool for the simultaneous visualization of interconnected molecular features in heatmaps of multi-omics data sets. multiSLIDE visualizes biologically connected molecular features by keyword search of pathways or genes, offering convenient functionalities to query, rearrange, filter, and cluster data on a web browser in real time. Various querying mechanisms make it adaptable to diverse omics types, and visualizations are customizable. We demonstrate the versatility of multiSLIDE through three examples, showcasing its applicability to a wide range of multi-omics data sets, by allowing users to visualize established links between molecules from different omics data, as well as incorporate custom inter-molecular relationship information into the visualization. Online and stand-alone versions of multiSLIDE are available at https://github.com/soumitag/multiSLIDE.
Direct electron detectors are a recent breakthrough in transmission electron microscopy that have opened up the possibility of super-resolution microscopy even at low doses. These detectors use CMOS sensors that allow fast read-outs, such that individual electron events (the "puddles" formed by the secondary electrons) can be recorded.While single event detection based imaging, referred to as electron counting, is starting to be widely adopted, several challenges still remain. One of these is, accurately identifying the entry point of the primary electron given the secondary electron puddle produced by it. Succeeding here reduces imaging noise, improves detector efficiency and allows for super-pixel accurate reconstruction [1]. It has been shown that these secondary electron puddles can vary greatly in shape and size [2]. While several techniques have been proposed [2], there is no consensus on which of these is optimal and why they would be better. Here, we investigate the shape and size of these secondary electron puddles to better understand how electron counting can be improved.We present results from several shadow experiments, where a beam blanker is used to block a part of the electron beam, performed using the DE-16 detector (Direct Electron, LP, San Diego, CA, USA) on a JEM-2200FS transmission electron microscope (JEOL USA Inc, Peabody, MA, USA). These experiments are used to study the differences between the secondary electron puddles in the exposed region and the shadow of the beam blanker (Fig. 1). Indeed in our experiments significant number of secondary electron puddles could be seen in the shadow region, which was previously conjectured to arise from electrons scattered back into the detector from the detector's surface, electrons scattered by the microscope column, and Xray photons generated when electrons are absorbed by the beam blanker and the microscope column [3].We found a statistically significant difference between the distribution of sizes of secondary electron puddles in the exposed and shadow regions (Fig. 2a). The puddles in the shadow region have larger variance in size than puddles in the exposed region. Although the secondary electron puddles vary greatly in shape, they appear to share common morphological features (Fig. 2c,d). Further, there appears no statistically significant differences in the shape of electron puddles found in the exposed versus shadow regions. We quantify the frequency of such stray electrons for the DE-16 detector (Fig. 2b), and speculate on possible strategies for noise reduction.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.