Thomas S. Spisz

Automated sizing of DNA fragments in atomic force microscope images.

Current techniques used to measure lengths of DNA fragments in atomic force microscope (AFM) images require a user to operate interactive software and execute tedious error-prone cursor selections. An algorithm is proposed which provides an automated method for determining DNA fragment lengths from AFM images without interaction from the computer operator (e.g. cursor selections or mouse clicks). The approach utilises image processing techniques tailored to characteristics of AFM images of DNA fragments. The automated measurements have a mean absolute deviation of less than 1 pixel when compared to manual image-based measurements. The DNA length determined from the histogram of calculated lengths is accurate to within 3% of the actual DNA length in solution. For fragments that are 250 base-pairs long, the precision is estimated to be within 17 nm, which is about 20% of the total length. This precision was confirmed when the algorithm easily resolved fragments in one image that differed by only 17 nm. Fragment sizes up to 2000 base-pairs have been tested and successfully sized. This algorithm is being developed as part of a new solid-state DNA sizing technique for applications such as genotyping and construction of physical genome maps.

HYTHIRM Radiance Modeling and Image Analyses in Support of STS-119, STS-125 and STS-128 Space Shuttle Hypersonic Re-entries

We provide the first geometrically accurate (i.e., 3-D) temperature maps of the entire windward surface of the Space Shuttle during hypersonic reentry. To accomplish this task we began with estimated surface temperatures derived from CFD models at integral high Mach numbers and used them, the Shuttle’s surface properties and reasonable estimates of the sensor-to-target geometry to predict the emitted spectral radiance from the surface (in units of W sr -1 m -2 nm -1 ). These data were converted to sensor counts using properties of the sensor (e.g. aperture, spectral band, and various efficiencies), the expected background, and the atmosphere transmission to inform the optimal settings for the near-infrared and midwave IR cameras on the Cast Glance aircraft. Once these data were collected, calibrated, edited, registered and co-added we formed both 2-D maps of the scene in the above units and 3-D maps of the bottom surface in temperature that could be compared with not only the initial inputs but also thermocouple data from the Shuttle itself. The 3-D temperature mapping process was based on the initial radiance modeling process. Here temperatures were “guessed” for each node in a well-resolved 3-D framework, a radiance model was produced and compared to the processed imagery, and corrections to the temperature were estimated until the iterative process converged. This process did very well in characterizing the temperature structure of the large asymmetric boundary layer transition the covered much of the starboard bottom surface of STS-119 Discovery. Both internally estimated accuracies and differences with CFD models and thermocouple measurements are at most a few percent. The technique did less well characterizing the temperature structure of the turbulent wedge behind the trip due to limitations in understanding the true sensor resolution. (Note: Those less inclined to read the entire paper are encouraged to read an Executive Summary provided at the end.)

Processing near-infrared imagery of hypersonic space shuttle reentries

High-resolution, calibrated, near-infrared imagery of the Space Shuttle during reentry has been obtained by a US Navy NP-3D Orion aircraft as part of NASAs HYTHIRM (Hypersonic Thermodynamic InfraRed Measurements) project. The long-range optical sensor package is called Cast Glance. Three sets of imagery have been processed thus far: 1) STS- 119 when Shuttle Discovery was at 52 km away at Mach 8.4, 2) STS-125 when Shuttle Atlantis was 71 km away at Mach 14.3, and 3) STS-128 when Shuttle Discovery was at 80 km away at Mach 14.7. The challenges presented in processing a manually-tracked high-angular rate, air-to-air image data collection include management of significant frame-to-frame motions, motion-induced blurring, changing orientations and ranges, daylight conditions, and sky backgrounds (including some cirrus clouds). This paper describes processing the imagery to estimate Shuttle surface temperatures. Our goal is to reduce the detrimental effects due to motions (sensor and Shuttle), vibration, and atmospherics for image quality improvement, without compromising the quantitative integrity of the data, especially local intensity variations. Our approach is to select and utilize only the highest quality images, register many cotemporal image frames to a single image frame, and then add the registered frames to improve image quality and reduce noise. These registered and averaged intensity images are converted to temperatures on the Shuttles windward surface using a series of steps starting with preflight calibration data. Comparisons with thermocouples at different points along the space Shuttle and between the three reentries will be shown.

Global Thermography of the Space Shuttle During Hypersonic Re-entry

Three dimensional surface thermography of the windward side of the Space Shuttle based on near infrared measurements is presented for STS-119, STS-125, STS-128, STS-132 and STS-133 reentries. A method used to project 2-D imagery to 3-D surface geometry is used to improve on previously used iterative method both in accuracy and in computational speed. Effects of material dependent surface spectral emissivities, image blurring and image-model alignment are all seen to have strong effects on the resultant temperature map. Results indicate best surface temperature accuracies in regions of small thermal gradients. Acronyms

Detection of gas plumes in cluttered environments using long-wave infrared hyperspectral sensors

Long-wave infrared hyperspectral sensors provide the ability to detect gas plumes at stand-off distances. A number of detection algorithms have been developed for such applications, but in situations where the gas is released in a complex background and is at air temperature, these detectors can generate a considerable amount of false alarms. To make matters more difficult, the gas tends to have non-uniform concentrations throughout the plume making it spatially similar to the false alarms. Simple post-processing using median filters can remove a number of the false alarms, but at the cost of removing a significant amount of the gas plume as well. We approach the problem using an adaptive subpixel detector and morphological processing techniques. The adaptive subpixel detection algorithm is able to detect the gas plume against the complex background. We then use morphological processing techniques to isolate the gas plume while simultaneously rejecting nearly all false alarms. Results will be demonstrated on a set of ground-based long-wave infrared hyperspectral image sequences.

Length determination of DNA fragments in atomic force microscope images

A processing algorithm was developed to detect and determine the lengths of DNA fragments in atomic force microscope images. The algorithm was designed to account for varying image conditions, fragment sizes, and background contamination, while minimizing the processing time to provide a high throughput. Although a large enough sample of images has not been tested yet to determine precisely the accuracy, we estimate the accuracy to be within 2 pixels based on analysis of an ideal simulated image and an actual image.

Measurement of bone mineral density in space

The purpose of the Advanced Multiple Projection Dual Energy X-ray Absorptiometry (AMPDXA) Scanning System project is to design, build, and test a precision scanner system for monitoring the deleterious effects of weightlessness on the human musculoskeletal system during prolonged spaceflight. The instrument uses dual energy X-ray absorptiometry (DXA) principles and is designed to measure bone mineral density (BMD), decompose soft tissue into fat and muscle, and derive structural properties (cross-sections, moments of inertia). Such data permits assessment of microgravity effects on bone and muscle and the associated fracture risk upon returning to planetary gravity levels. Multiple projections, coupled with axial translation, provide three-dimensional geometric properties suitable for accurate structural analysis. This structural analysis, coupled with bone models and estimated loads, defines the fracture risk. The scanner will be designed to minimize volume and mass (46-kg goal), while maintaining the required mechanical stability for high-precision measurement. The AMPDXA will be able to detect changes less than 1% in bone mass and geometry and changes less than 5% in muscle mass.

Processing ground-based near-infrared imagery of space shuttle re-entries

Ground-based high-resolution, calibrated, near-infrared (NIR) imagery of the Space Shuttle STS-134 Endeavour during reentry has been obtained as part of NASAs HYTHIRM (Hypersonic Thermodynamic InfraRed Measurements) project. The long-range optical sensor package called MARS (Mobile Aerospace Reconnaissance System) was positioned in advance to acquire and track part of the shuttle re-entry. Imagery was acquired during a few minutes, with the best imagery being processed when the shuttle was at 133 kft at Mach 5.8. This paper describes the processing of the NIR imagery, building upon earlier work from the airborne imagery collections of several prior shuttle missions. Our goal is to calculate the temperature distribution of the shuttles bottom surface as accurately as possible, considering both random and systematic errors, while maintaining all physical features in the imagery, especially local intensity variations. The processing areas described are: 1) radiometric calibration, 2) improvement of image quality, 3) atmospheric compensation, and 4) conversion to temperature. The computed temperature image will be shown, as well as comparisons with thermocouples at different positions on the shuttle. A discussion of the uncertainties of the temperature estimates using the NIR imagery is also given.

Assimilation of nontraditional datasets to improve atmospheric compensation

Detection and characterization of space objects require the capability to derive physical properties such as brightness temperature and reflectance. These quantities, together with trajectory and position, are often used to correlate an object from a catalogue of known characteristics. However, retrieval of these physical quantities can be hampered by the radiative obscuration of the atmosphere. Atmospheric compensation must therefore be applied to remove the radiative signature of the atmosphere from electro-optical (EO) collections and enable object characterization. The JHU/APL Atmospheric Compensation System (ACS) was designed to perform atmospheric compensation for long, slant-range paths at wavelengths from the visible to infrared. Atmospheric compensation is critically important for airand ground-based sensors collecting at low elevations near the Earths limb. It can be demonstrated that undetected thin, sub-visual cirrus clouds in the line of sight (LOS) can significantly alter retrieved target properties (temperature, irradiance). The ACS algorithm employs non-traditional cirrus datasets and slant-range atmospheric profiles to estimate and remove atmospheric radiative effects from EO/IR collections. Results are presented for a NASA-sponsored collection in the near-IR (NIR) during hypersonic reentry of the Space Shuttle during STS-132.

Determination of bone structural parameters from multiple projection DXA images

To more precisely measure and monitor bone health, The Johns Hopkins University Applied Physics Lab and School of Medicine have developed the Advanced Multiple Projection Dual-Energy X-Ray Absorptiometry (AMPDXA) scanner. This system provides improvements over conventional DXA scanners in image resolution and multiple projection capability. These improvements allow us to determine structural information about the bone in addition to the standard bone mineral density (BMD) measurements. Algorithms and software were developed to process data acquired from the AMPDXA scanner and to determine important structural parameters, such as the center of mass axis in three dimensions and cross-sectional moments of inertia. The analysis operates on three projections about 15 degrees apart, calculates BMD for each projection, and then combines the data into a three dimensional coordinate system. By knowing the patient position in three dimensions, bone structural parameters are calculated more precisely. Using repeated testing of cadaver bones, the precision of determining these structural parameters is approximately the detector pixel size of 0.127 mm. Data on artificial bone cylinders indicate accuracy of about 3%. Comparisons between bone structural parameters derived from AMPDXA and CT scans show very similar results.