We capture ssTEM data using SerialEM software developed by D. Mastronarde at the University of Colorado at Boulder [72 (link)]. Though originally developed for TEM tomography, SerialEM is ideal for large-scale mosaicking. The most recent build version of SerialEM allows definition of multiple circular or polygonal regions of interest on a grid and automates stage drive and image capture within the regions of interest on the JEOL JEM 1400 TEM (and other recent TEMs as well such as FEI Tecnais) and, critically, stores stage position metadata for each tile. This greatly reduces the computational cost of the initial positioning of mosaic tiles from O(n2) to O(n). The program includes a scripting capability that provides the flexibility needed to optimize the acquisition strategy, for example, by focusing only on an appropriately spaced subset of the image tiles. While automated capture is ideal for the microscope's Gatan Ultrascan 4000 (4K × 4K) camera, it can also serve on a smaller scale with film capture.
Automated Mosaic Imaging for CN Map
We capture ssTEM data using SerialEM software developed by D. Mastronarde at the University of Colorado at Boulder [72 (link)]. Though originally developed for TEM tomography, SerialEM is ideal for large-scale mosaicking. The most recent build version of SerialEM allows definition of multiple circular or polygonal regions of interest on a grid and automates stage drive and image capture within the regions of interest on the JEOL JEM 1400 TEM (and other recent TEMs as well such as FEI Tecnais) and, critically, stores stage position metadata for each tile. This greatly reduces the computational cost of the initial positioning of mosaic tiles from O(n2) to O(n). The program includes a scripting capability that provides the flexibility needed to optimize the acquisition strategy, for example, by focusing only on an appropriately spaced subset of the image tiles. While automated capture is ideal for the microscope's Gatan Ultrascan 4000 (4K × 4K) camera, it can also serve on a smaller scale with film capture.
Corresponding Organization : University of Colorado Boulder
Protocol cited in 12 other protocols
Variable analysis
- Capturing ssTEM data using SerialEM software
- Defining multiple circular or polygonal regions of interest on a grid
- Automating stage drive and image capture within the regions of interest on the JEOL JEM 1400 TEM (and other recent TEMs as well such as FEI Tecnais)
- Storing stage position metadata for each tile
- Number of images or tiles captured per section (950–1,100)
- Number of sections captured (≈333)
- Thickness of sections (70–90 nm)
- Time required for capture (30 s/frame, 70–100 calendar days on a single TEM)
- Storage required for unprocessed 16-bit images (10.4 terabytes)
- Overlap between adjacent images (15% area overlap)
- Magnification (5,000×)
- No positive or negative controls were explicitly mentioned in the given information.
Annotations
Based on most similar protocols
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!