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Title: Dynamic scan control in STEM: Spiral scans

Abstract

Here, scanning transmission electron microscopy (STEM) has emerged as one of the foremost techniques to analyze materials at atomic resolution. However, two practical difficulties inherent to STEM imaging are: radiation damage imparted by the electron beam, which can potentially damage or otherwise modify the specimen and slow-scan image acquisition, which limits the ability to capture dynamic changes at high temporal resolution. Furthermore, due in part to scan flyback corrections, typical raster scan methods result in an uneven distribution of dose across the scanned area. A method to allow extremely fast scanning with a uniform residence time would enable imaging at low electron doses, ameliorating radiation damage and at the same time permitting image acquisition at higher frame-rates while maintaining atomic resolution. The practical complication is that rastering the STEM probe at higher speeds causes significant image distortions. Non-square scan patterns provide a solution to this dilemma and can be tailored for low dose imaging conditions. Here, we develop a method for imaging with alternative scan patterns and investigate their performance at very high scan speeds. A general analysis for spiral scanning is presented here for the following spiral scan functions: Archimedean, Fermat, and constant linear velocity spirals, which were testedmore » for STEM imaging. The quality of spiral scan STEM images is generally comparable with STEM images from conventional raster scans, and the dose uniformity can be improved.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Sciences (CNMS)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1256773
Grant/Contract Number:
AC05-00OR22725
Resource Type:
Journal Article: Published Article
Journal Name:
Advanced Structural and Chemical Imaging
Additional Journal Information:
Journal Volume: 2; Journal Issue: 1; Journal ID: ISSN 2198-0926
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; aberration-corrected STEM; scan control; distortion; spiral scan

Citation Formats

Lupini, Andrew R., Borisevich, Albina Y., Kalinin, Sergei V., Endeve, Eirik, Archibald, Richard K., Jesse, Stephen, Sang, Xihan, Unocic, Raymond R., and Chi, Miaofang. Dynamic scan control in STEM: Spiral scans. United States: N. p., 2016. Web. doi:10.1186/s40679-016-0020-3.
Lupini, Andrew R., Borisevich, Albina Y., Kalinin, Sergei V., Endeve, Eirik, Archibald, Richard K., Jesse, Stephen, Sang, Xihan, Unocic, Raymond R., & Chi, Miaofang. Dynamic scan control in STEM: Spiral scans. United States. doi:10.1186/s40679-016-0020-3.
Lupini, Andrew R., Borisevich, Albina Y., Kalinin, Sergei V., Endeve, Eirik, Archibald, Richard K., Jesse, Stephen, Sang, Xihan, Unocic, Raymond R., and Chi, Miaofang. 2016. "Dynamic scan control in STEM: Spiral scans". United States. doi:10.1186/s40679-016-0020-3.
@article{osti_1256773,
title = {Dynamic scan control in STEM: Spiral scans},
author = {Lupini, Andrew R. and Borisevich, Albina Y. and Kalinin, Sergei V. and Endeve, Eirik and Archibald, Richard K. and Jesse, Stephen and Sang, Xihan and Unocic, Raymond R. and Chi, Miaofang},
abstractNote = {Here, scanning transmission electron microscopy (STEM) has emerged as one of the foremost techniques to analyze materials at atomic resolution. However, two practical difficulties inherent to STEM imaging are: radiation damage imparted by the electron beam, which can potentially damage or otherwise modify the specimen and slow-scan image acquisition, which limits the ability to capture dynamic changes at high temporal resolution. Furthermore, due in part to scan flyback corrections, typical raster scan methods result in an uneven distribution of dose across the scanned area. A method to allow extremely fast scanning with a uniform residence time would enable imaging at low electron doses, ameliorating radiation damage and at the same time permitting image acquisition at higher frame-rates while maintaining atomic resolution. The practical complication is that rastering the STEM probe at higher speeds causes significant image distortions. Non-square scan patterns provide a solution to this dilemma and can be tailored for low dose imaging conditions. Here, we develop a method for imaging with alternative scan patterns and investigate their performance at very high scan speeds. A general analysis for spiral scanning is presented here for the following spiral scan functions: Archimedean, Fermat, and constant linear velocity spirals, which were tested for STEM imaging. The quality of spiral scan STEM images is generally comparable with STEM images from conventional raster scans, and the dose uniformity can be improved.},
doi = {10.1186/s40679-016-0020-3},
journal = {Advanced Structural and Chemical Imaging},
number = 1,
volume = 2,
place = {United States},
year = 2016,
month = 6
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1186/s40679-016-0020-3

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  • Here, scanning transmission electron microscopy (STEM) has emerged as one of the foremost techniques to analyze materials at atomic resolution. However, two practical difficulties inherent to STEM imaging are: radiation damage imparted by the electron beam, which can potentially damage or otherwise modify the specimen and slow-scan image acquisition, which limits the ability to capture dynamic changes at high temporal resolution. Furthermore, due in part to scan flyback corrections, typical raster scan methods result in an uneven distribution of dose across the scanned area. A method to allow extremely fast scanning with a uniform residence time would enable imaging atmore » low electron doses, ameliorating radiation damage and at the same time permitting image acquisition at higher frame-rates while maintaining atomic resolution. The practical complication is that rastering the STEM probe at higher speeds causes significant image distortions. Non-square scan patterns provide a solution to this dilemma and can be tailored for low dose imaging conditions. Here, we develop a method for imaging with alternative scan patterns and investigate their performance at very high scan speeds. A general analysis for spiral scanning is presented here for the following spiral scan functions: Archimedean, Fermat, and constant linear velocity spirals, which were tested for STEM imaging. The quality of spiral scan STEM images is generally comparable with STEM images from conventional raster scans, and the dose uniformity can be improved.« less
  • There is widespread acceptance of the thesis that in a patient with suspected embolism, a normal perfusion lung scan excludes the diagnosis of acute pulmonary embolism. However, limited published data exist which validate this thesis. We have explored this question by longitudinal follow-up of 68 patients who were referred for lung scanning to rule out embolism and proved to have normal perfusion lung scans. Risk factors for venous thromboembolism among these patients were similar to those reported in prior series of patients with pulmonary embolism. Our data support the widely-held views that: 1) a normal perfusion lung scan excludes themore » diagnosis of clinically significant pulmonary emboli; 2) the diagnostic work-up for suspected pulmonary embolism need not extend beyond a normal perfusion scan; 3) anticoagulant therapy can be discontinued after a normal perfusion scan, except in the presence of documented venous thrombosis; and 4) a normal lung scan has the same value in ruling out embolism in man as does a normal pulmonary angiogram.« less
  • The usual time interval between the administration of technetium-labeled bone-seeking radiopharmaceuticals and imaging varies among nuclear-medical departments. Pharmacokinetic data indicate that the interval could be as short as 2 hr. We have studied overall quality of bone detail in 280 bone scans performed at intervals varying from 2 to 5 hr following injection of technetium-99m diphosphonate. No significant qualitative difference was found between the studies performed at 2 hr and those done at later intervals.
  • Purpose: Four-dimensional (4D) respiration-correlated imaging techniques can be used to obtain (respiration) artifact-free computed tomography (CT) images of the thorax. Current radiotherapy planning systems, however, do not accommodate 4D-CT data. The purpose of this study was to develop a simple, new concept to incorporate patient-specific motion information, using 4D-CT scans, in the radiotherapy planning process of lung cancer patients to enable smaller error margins. Methods and Materials: A single CT scan was selected from the 4D-CT data set. This scan represented the tumor in its time-averaged position over the respiratory cycle (the mid-ventilation CT scan). To select the appropriate CTmore » scan, two methods were used. First, the three-dimensional tumor motion was analyzed semiautomatically to calculate the mean tumor position and the corresponding respiration phase. An alternative automated method was developed to select the correct CT scan using the diaphragm motion. Results: Owing to hysteresis, mid-ventilation selection using the three-dimensional tumor motion had a tumor position accuracy (with respect to the mean tumor position) better than 1.1 {+-} 1.1 mm for all three directions (inhalation and exhalation). The accuracy in the diaphragm motion method was better than 1.1 {+-} 1.1 mm. Conventional free-breathing CT scanning had an accuracy better than 0 {+-} 3.9 mm. The mid-ventilation concept can result in an average irradiated volume reduction of 20% for tumors with a diameter of 40 mm. Conclusion: Tumor motion and the diaphragm motion method can be used to select the (artifact-free) mid-ventilation CT scan, enabling a significant reduction of the irradiated volume.« less
  • Purpose: To characterize the effect of deformable registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (≥60Gy, 2Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pre-therapy (4–75 days) CT scan and a treatment planning scan with an associated dose map calculated in Pinnacle were collected. To establish baseline correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pre-therapy scans were co-registered with planning scans (and associated dose maps)more » using the Plastimatch demons and Fraunhofer MEVIS deformable registration algorithms. Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from both registration algorithms. The absolute difference in planned dose (|ΔD|) between manually and automatically mapped landmark points was calculated. Using regression modeling, |ΔD| was modeled as a function of the distance between manually and automatically matched points (registration error, E), the dose standard deviation (SD-dose) in the eight-pixel neighborhood, and the registration algorithm used. Results: 52–92 landmark point pairs (median: 82) were identified in each patient's scans. Average |ΔD| across patients was 3.66Gy (range: 1.2–7.2Gy). |ΔD| was significantly reduced by 0.53Gy using Plastimatch demons compared with Fraunhofer MEVIS. |ΔD| increased significantly as a function of E (0.39Gy/mm) and SD-dose (2.23Gy/Gy). Conclusion: An average error of <4Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration. Dose differences following registration were significantly increased when the Fraunhofer MEVIS registration algorithm was used, spatial registration errors were larger, and dose gradient was higher (i.e., higher SD-dose). To our knowledge, this is the first study to directly compute dose errors following deformable registration of lung CT scans.« less