SPECTROMICROSCOPY OF BIOLOGICAL AND ENVIRONMENTAL SYSTEMS AT STONY BROOK: INSTRUMENTATION AND ANALYSIS

2002 ◽  
Vol 09 (01) ◽  
pp. 185-191 ◽  
Author(s):  
C. JACOBSEN ◽  
T. BEETZ ◽  
M. FESER ◽  
A. OSANNA ◽  
A. STEIN ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Data Analysis ◽  
Environmental Science ◽  
National Laboratory ◽  
Principal Component ◽  
Brookhaven National Laboratory ◽  
National Synchrotron Light Source ◽  
X Ray ◽  
Synchrotron Light ◽  
Data Analysis Methods

Soft X-ray microscopy allows one to study nanoscale heterogeneities in dry and wet environmental science, biological, polymer, and geochemical specimens. Recent advances in instrumentation at the X-1A beamline at the National Synchrotron Light Source at Brookhaven National Laboratory are described. Spectromicroscopy data analysis methods including component mapping and principal component analysis (PCA) are then discussed.

Imaging, Spectroscopy and Tomography of Frozen Hydrated Specimens With the Cryo Scanning Transmission X-Ray Microscope at The NSLS

1998 ◽  
Vol 4 (S2) ◽  
pp. 354-355
Author(s):  
J. Maser ◽  
C. Jacobsen ◽  
Y. Wang ◽  
A. Osanna ◽  
B. Winn ◽  
...  
Keyword(s):  
National Laboratory ◽  
Imaging Spectroscopy ◽  
Optical Resolution ◽  
Brookhaven National Laboratory ◽  
X Rays ◽  
X Ray ◽  
Measuring Techniques ◽  
Steady Improvement ◽  
Scanning Transmission ◽  
Synchrotron Light

With the steady improvement of x-ray optics with high resolution and efficiency, and continued development or adaptation of different imaging and measuring techniques, soft x-ray microscopy has emerged as a powerful method to image and analyze fully hydrated specimens of several micrometer thickness at sub-optical resolution (for a recent overview, see ref. 1). We report on experiments performed with the cryo scanning transmission x-ray microscope (cryo-STXM), which has recently come into operation at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory.Cryo-STXM uses x-rays with energies between the absorption edge of Carbon (E = 284 eV) and Oxygen (E = 543 eV) from the soft x-ray undulator at the NSLS. Fully hydrated specimens such as eucaryotic cells in water or ice layers of up to 10 micrometer thickness can be imaged without any additional need for contrast enhancing techniques.

Expression, purification, crystallization and preliminary X-ray analysis of Escherichia coli argininosuccinate synthetase

1999 ◽  
Vol 55 (12) ◽  
pp. 2028-2030 ◽  
Author(s):  
Chris Lemke ◽  
Melissa Yeung ◽  
P. Lynne Howell
Keyword(s):  
Escherichia Coli ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
Argininosuccinate Synthetase ◽  
Affinity Tag ◽  
X Ray ◽  
Diffusion Technique ◽  
Cell Dimensions ◽  
Synchrotron Light ◽  
Unit Cell Dimensions

A recombinant form of Escherichia coli argininosuccinate synthetase with a C-terminal polyhistidine affinity tag has been expressed, purified and subsequently crystallized using the hanging-drop vapour-diffusion technique. The crystals grow as large rectangular chunks with unit-cell dimensions a = 79.70, b = 105.84, c = 127.33 Å, α = β = γ = 90°. The crystals exhibit the symmetry of space group I222 and diffract to a minimum d-spacing of 1.6 Å at station X8C of the National Synchrotron Light Source, Brookhaven National Laboratory. On the basis of density calculations, one monomer of this homotetrameric protein is predicted per asymmetric unit (Matthews coefficient Vm = 2.69 Å3 Da−1).

Development and testing of stable supports for the National Synchrotron Light Source II RF beam position monitors

2010 ◽  
Vol 1 (MEDSI-6) ◽  
Author(s):  
B. Kosciuk ◽  
V. Ravindranath ◽  
O. Singh ◽  
S. Sharma
Keyword(s):  
Light Source ◽  
Coefficient Of Thermal Expansion ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
National Synchrotron Light Source ◽  
Beam Position ◽  
Vacuum Chambers ◽  
Synchrotron Light ◽  
Under Construction ◽  
Beam Position Monitors

The National Synchrotron Light Source II currently under construction at the Brookhaven National Laboratory is expected to provide unprecedented orbit stability in the storage ring in order to fully utilize the very small emittance of the electron beam. The desire to measure the position of such small beams to high resolution imposes stringent requirements on the thermal and structural stability of the supports for the beam postion monitor (BPM) pick-up electrodes located on multi-pole vacuum chambers and more so on those located upstream and downstream of insertion device sources where the beam size is the smallest. Even with tunnel air temperature expected to be controlled to ±0.1°C, low coefficient of thermal expansion materials is required to meet this level of thermal stability. Here, we present the application of these materials to the design of stable supports for radio frequency (RF)-BPMs as well as the methods of testing their performance.

MANTiS: a program for the analysis of X-ray spectromicroscopy data

2014 ◽  
Vol 21 (5) ◽  
pp. 1206-1212 ◽  
Author(s):  
Mirna Lerotic ◽  
Rachel Mak ◽  
Sue Wirick ◽  
Florian Meirer ◽  
Chris Jacobsen
Keyword(s):  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Data Analysis ◽  
Principal Component ◽  
Analysis Tool ◽  
X Ray ◽  
Manual Analysis ◽  
X Ray Imaging ◽  
Data Analysis Tool ◽  
And Cluster Analysis

Spectromicroscopy combines spectral data with microscopy, where typical datasets consist of a stack of images taken across a range of energies over a microscopic region of the sample. Manual analysis of these complex datasets can be time-consuming, and can miss the important traits in the data. With this in mind we have developedMANTiS, an open-source tool developed in Python for spectromicroscopy data analysis. The backbone of the package involves principal component analysis and cluster analysis, classifying pixels according to spectral similarity. Our goal is to provide a data analysis tool which is comprehensive, yet intuitive and easy to use.MANTiSis designed to lead the user through the analysis using story boards that describe each step in detail so that both experienced users and beginners are able to analyze their own data independently. These capabilities are illustrated through analysis of hard X-ray imaging of iron in Roman ceramics, and soft X-ray imaging of a malaria-infected red blood cell.

Overview of diagnostics and instrumentation for National Synchrotron Light Source II

2010 ◽  
Vol 1 (MEDSI-6) ◽  
Author(s):  
B. Kosciuk ◽  
A. Blednykh ◽  
D. Padrazo ◽  
O. Singh
Keyword(s):  
Light Source ◽  
State Of The Art ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
Beam Diagnostics ◽  
Third Generation ◽  
National Synchrotron Light Source ◽  
Beam Stability ◽  
Synchrotron Light ◽  
Under Construction

National Synchrotron Light Source II (NSLS-II), a new state-of-the-art third-generation light source under construction at Brookhaven National Laboratory is expected to have extremely small emittance and extraordinary beam stability. The mechanical requirements for beam diagnostics and instrumentation are exceptionally challenging. Here we present an overview of the mechanical aspects of some NSLS-II diagnostics as well as the performance levels of some systems currently under development.

The NSLS X-1AL scanning x-ray microscope

1993 ◽  
Vol 51 ◽  
pp. 636-637
Author(s):  
Chris Jacobsen ◽  
Janos Kirz ◽  
Steve Lindaas ◽  
Sue Wirick ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
Fresnel Zone ◽  
National Laboratory ◽  
Photon Counting ◽  
Brookhaven National Laboratory ◽  
Dark Field ◽  
X Rays ◽  
High Brightness ◽  
X Ray ◽  
Synchrotron Light ◽  
Dose Imaging

Soft x rays are well suited to the study of low-Z elements in 0.1-10 μm thick specimens. A variety of soft x-ray microscopes are now under operation, several of which achieve image resolutions of 0.03-0.1 μm. Scanning x-ray microscopes offer some desirable charactistics: they are able to operate in a variety of imaging modes, including transmission, luminescence, dark field, and photoemission, and they enable minimum dose imaging by utilizing highly efficient photon counting detectors and placing moderate efficiency optics between the source and specimen rather than between specimen and detector.The NSLS X-1AL scanning x-ray microscope uses an undulator at the National Synchrotron Light Source at Brookhaven National Laboratory as a tunable, high-brightness soft x-ray source. Monochromatized, spatially coherent illumination is focussed by a Fresnel zone plate fabricated using electron beam lithography. The sample is scanned through the 0.055 μm Rayleigh resolution focal spot using stepping motors (for large scans) and linearized piezos.

Laura Mgrdichian National Synchrotron Light Source, Brookhaven National Laboratory

2004 ◽  
Vol 17 (5) ◽  
pp. 13-29
Author(s):  
Laura Mgrdichian ◽  
Arhonda Gogos ◽  
Peter W. Stephens ◽  
Lawrence Shapiro ◽  
D. Peter Siddons ◽  
...  
Keyword(s):  
Light Source ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
National Synchrotron Light Source ◽  
Synchrotron Light
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