Biophotonic Tools in Cell and Tissue Diagnostics.

In order to maintain the rapid advance of biophotonics in the U.S. and enhance our competitiveness worldwide, key measurement tools must be in place. As part of a wide-reaching effort to improve the U.S. technology base, the National Institute of Standards and Technology sponsored a workshop titled "Biophotonic tools for cell and tissue diagnostics." The workshop focused on diagnostic techniques involving the interaction between biological systems and photons. Through invited presentations by industry representatives and panel discussion, near- and far-term measurement needs were evaluated. As a result of this workshop, this document has been prepared on the measurement tools needed for biophotonic cell and tissue diagnostics. This will become a part of the larger measurement road-mapping effort to be presented to the Nation as an assessment of the U.S. Measurement System. The information will be used to highlight measurement needs to the community and to facilitate solutions

The VIMOS Integral Field Unit: data reduction methods and quality assessment

With new generation spectrographs integral field spectroscopy is becoming a widely used observational technique. The Integral Field Unit of the VIsible Multi-Object Spectrograph on the ESO-VLT allows to sample a field as large as 54" x 54" covered by 6400 fibers coupled with micro-lenses. We are presenting here the methods of the data processing software developed to extract the astrophysical signal of faint sources from the VIMOS IFU observations. We focus on the treatment of the fiber-to-fiber relative transmission and the sky subtraction, and the dedicated tasks we have built to address the peculiarities and unprecedented complexity of the dataset. We review the automated process we have developed under the VIPGI data organization and reduction environment (Scodeggio et al. 2005), along with the quality control performed to validate the process. The VIPGI-IFU data processing environment is available to the scientific community to process VIMOS-IFU data since November 2003.Comment: 19 pages, 10 figures and 1 table. Accepted for publication in PAS

The XMM-Newton view of the Crab

Aims. We discuss the current X-ray view of the Crab Nebula and Pulsar, summarising our analysis of observations of the source with the EPIC-pn camera on board the XMM-Newton observatory. Different modes of EPIC-pn were combined in order to yield a complete scenario of the spectral properties of the Crab resolved in space and time (pulse phase). In addition we give a description of the special EPIC-pn Burst mode and guidance for data reduction in that mode. Methods. We analysed spectra for the nebula and pulsar separately in the 0.6−12.0 keV energy band. All data were processed with the SAS 6.0.0 XMM-Newton Scientific Analysis System package; models were fitted to the data with XSPEC 11. The high time resolution of EPIC-pn in its Burst mode (7 μs) was used for a phase resolved analysis of the pulsar spectrum, after determination of the period with epoch folding techniques. Data from the SmallWindow mode were processed and corrected for pile-up allowing for spectroscopy simultaneously resolved in space and time. Results. The spatial variation of the spectrum over the entire region of the Crab shows a gradual spectral softening from the inner pulsar region to the outer nebula region with a variation in photon index, Γ, from 2.0 to 2.4. Pulse phase resolved spectroscopy of the Crab Pulsar reveals a phase dependent modulation of the photon index in form of a significant hardening of the spectrum in the inter-peak phase from Γ = 1.7 during the pulse peak to Γ = 1.5

Review of small-angle coronagraphic techniques in the wake of ground-based second-generation adaptive optics systems

Small-angle coronagraphy is technically and scientifically appealing because it enables the use of smaller telescopes, allows covering wider wavelength ranges, and potentially increases the yield and completeness of circumstellar environment - exoplanets and disks - detection and characterization campaigns. However, opening up this new parameter space is challenging. Here we will review the four posts of high contrast imaging and their intricate interactions at very small angles (within the first 4 resolution elements from the star). The four posts are: choice of coronagraph, optimized wavefront control, observing strategy, and post-processing methods. After detailing each of the four foundations, we will present the lessons learned from the 10+ years of operations of zeroth and first-generation adaptive optics systems. We will then tentatively show how informative the current integration of second-generation adaptive optics system is, and which lessons can already be drawn from this fresh experience. Then, we will review the current state of the art, by presenting world record contrasts obtained in the framework of technological demonstrations for space-based exoplanet imaging and characterization mission concepts. Finally, we will conclude by emphasizing the importance of the cross-breeding between techniques developed for both ground-based and space-based projects, which is relevant for future high contrast imaging instruments and facilities in space or on the ground.Comment: 21 pages, 7 figure

Genome-inspired molecular identification in organic matter via Raman spectroscopy

Rapid, non-destructive characterization of molecular level chemistry for organic matter (OM) is experimentally challenging. Raman spectroscopy is one of the most widely used techniques for non-destructive chemical characterization, although it currently does not provide detailed identification of molecular components in OM, due to the combination of diffraction-limited spatial resolution and poor applicability of peak-fitting algorithms. Here, we develop a genome-inspired collective molecular structure fingerprinting approach, which utilizes ab initio calculations and data mining techniques to extract molecular level chemistry from the Raman spectra of OM. We illustrate the power of such an approach by identifying representative molecular fingerprints in OM, for which the molecular chemistry is to date inaccessible using non-destructive characterization techniques. Chemical properties such as aromatic cluster size distribution and H/C ratio can now be quantified directly using the identified molecular fingerprints. Our approach will enable non-destructive identification of chemical signatures with their correlation to the preservation of biosignatures in OM, accurate detection and quantification of environmental contamination, as well as objective assessment of OM with respect to their chemical contents

Laser Based Mid-Infrared Spectroscopic Imaging – Exploring a Novel Method for Application in Cancer Diagnosis

A number of biomedical studies have shown that mid-infrared spectroscopic images can provide both morphological and biochemical information that can be used for the diagnosis of cancer. Whilst this technique has shown great potential it has yet to be employed by the medical profession. By replacing the conventional broadband thermal source employed in modern FTIR spectrometers with high-brightness, broadly tuneable laser based sources (QCLs and OPGs) we aim to solve one of the main obstacles to the transfer of this technology to the medical arena; namely poor signal to noise ratios at high spatial resolutions and short image acquisition times. In this thesis we take the first steps towards developing the optimum experimental configuration, the data processing algorithms and the spectroscopic image contrast and enhancement methods needed to utilise these high intensity laser based sources. We show that a QCL system is better suited to providing numerical absorbance values (biochemical information) than an OPG system primarily due to the QCL pulse stability. We also discuss practical protocols for the application of spectroscopic imaging to cancer diagnosis and present our spectroscopic imaging results from our laser based spectroscopic imaging experiments of oesophageal cancer tissue