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Biomedical subjects

G T Herman

Publications and source records attributed to G T Herman.

At least 19 recordsLinked to original sources
PubMed2004

Transfer function restoration in 3D electron microscopy via iterative data refinement.

Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As with any other imaging device, the electron microscope introduces a transfer function (called in this field the contrast transfer function, CTF) into the image acquisition process that modulates the various frequencies of the signal. Thus, the 3D reconstructions performed with these CTF-affected projections are also affected by an implicit 3D transfer function. For high-resolution electron microscopy, the effect of the CTF is quite dramatic and limits severely the achievable resolution. In this work we make use of the iterative data refinement (IDR) technique to ameliorate the effect of the CTF. It is demonstrated that the approach can be successfully applied to noisy data.

Algorithms↗
PubMed2000

2.5-D simultaneous multislice reconstruction by series expansion methods from Fourier-rebinned PET data.

True three-dimensional (3-D) volume reconstruction from fully 3-D data in positron emission tomography (PET) has only a limited clinical use because of its large computational burden. Fourier rebinning (FORE) of the fully 3-D data into a set of 2-D sinogram data decomposes the 3-D reconstruction process into multiple 2-D reconstructions of decoupled 2-D image slices, thus substantially decreasing the computational burden even in the case when the 2-D reconstructions are performed by an iterative reconstruction algorithm. On the other hand, the approximations involved in the rebinning combined with the decoupling of the image slices cause a certain reduction of image quality, especially when the signal-to-noise ratio of the data is low. We propose a 2.5-D Simultaneous Multislice Reconstruction approach, based on the series expansion principle, where the volume is represented by the superposition of 3-D spherically symmetric bell-shaped basis functions. It takes advantage of the time reduction due to the use of the FORE (2-D) data, instead of the original fully 3-D data, but at the same time uses a 3-D iterative reconstruction approach with 3-D basis functions. The same general approach can be applied to any reconstruction algorithm belonging to the class of series expansion methods (iterative or noniterative) using 3-D basis functions that span multiple slices, and can be used for any multislice sinogram or list mode data whether obtained by a special rebinning scheme or acquired directly by a PET scanner in the 2-D mode using septa. Our studies confirm that the proposed 2.5-D approach provides a considerable improvement in reconstruction quality, as compared to the standard 2-D reconstruction approach, while the reconstruction time is of the same order as that of the 2-D approach and is clinically practical even on a general-purpose computer.

Algorithms↗
PubMed1999

Renal cyst pseudoenhancement: beam-hardening effects on CT numbers.

PURPOSE: To determine if simple renal cysts may be accurately characterized with helical computed tomography (CT) during peak levels of renal enhancement. MATERIALS AND METHODS: Water-filled "cysts" were suspended in varying concentrations of iodine solution, meant to simulate varying levels of renal enhancement, within an abdominal phantom. Volume-averaging effects were minimized by scanning cylindric 5-30-mm cysts with a helical technique (collimation, 5 mm; pitch, 1:1). Axial and helical techniques were then compared, and volume-averaging effects were evaluated by scanning 10- and 20-mm round cysts with 3-, 5-, and 7-mm collimation at background attenuation levels of 100 and 200 HU. RESULTS: Cylindric cyst attenuation increased consistently with increasing background attenuation. As background attenuation increased by 90 HU, attenuation increased by 11-17 HU in small (5- or 10-mm) cysts, and by 7-9 HU in large (15-30-mm) cysts. As background attenuation increased by 180 HU, attenuation increased by 18-28 HU in small cysts and by 10-15 HU in large cysts. Spherical cyst attenuation differences were maximized when smaller cysts were imaged with larger collimation, which is when volume-averaging effects became apparent. Axial and helical CT numbers did not differ substantially. Computer simulation studies showed that the observed effect could not be explained by beam hardening alone. CONCLUSION: Pseudoenhancement of renal cysts may occur if helical CT is performed during peak renal enhancement. CT algorithm modification may be necessary to correct for this effect, which is likely related to an inadequate algorithmic correction for beam hardening.

Kidney Diseases, Cystic↗
PubMed1999

Prediction of human observer performance by numerical observers: an experimental study.

Numerical observers are investigated for predicting the outcome of a free-response human observer study involving the detection of simulated pulmonary nodules in images reconstructed from low-dose computed tomography projection data by use of several reconstruction algorithms. A new way of calculating the figure of merit of a numerical observer is proposed wherein the detectability of signals in a particular image depends on the noise properties associated with that image and not the other images in the data set. The resulting variants of numerical observers are found to perform better than their traditional counterparts. In particular, the imagewise variant of the region-of-interest observer is found to predict best the rank ordering of algorithms by human observers for the free-response task.

Algorithms↗
PubMed1998

3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs).

Algebraic reconstruction techniques (ART) are iterative procedures for solving systems of linear equations. They have been used in tomography to recover objects from their projections. In this work we apply an ART approach in which the basis functions used to describe the objects are not based on voxels, but are much smoother functions named "blobs". The data collection studied in this work follows the so-called "conical tilt geometry" that is commonly used in many applications of three-dimensional electron microscopy of biological macromolecules. The performance of ART with blobs is carefully compared with a currently well-known three dimensional (3D) reconstruction algorithm (weighted back projection) using a methodology which assigns a level of statistical significance to a claim of relative superiority of one algorithm over another for a particular task. The conclusion we reach is that ART with blobs produces high-quality reconstructions and is, in particular, superior to weighted backprojection in recovering features along the "vertical" direction. For the exact implementation recommended in this paper, the computational costs of ART are almost an order of magnitude smaller than those of WBP.

Image Processing, Computer-Assisted↗
PubMed1997

Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection.

In this work we propose a reconstruction algorithm (ART with blobs) that has not been previously used in electron Tomography and we compare it with the standard method in the field (weighted back projection, WBP). We assume that only a limited set of very noisy images, collected around a single axis tilt, is available; which is a typical situation in Electron Tomography. In general, the reconstruction problem is underdetermined (due to the limited number of projections) and the data are inconsistent (due to the high level of noise). The evaluation of the results is performed in a rigorous way by a task-oriented approach which makes use of numerical observers. ART with blobs outperforms WBP for a number of key tasks. Results are presented both for simplified line integral data and for realistic simulations of macromolecular structures embedded in amorphous ice.

Algorithms↗
PubMed1994

A methodology for testing for statistically significant differences between fully 3D PET reconstruction algorithms.

We present a practical methodology for evaluating 3D PET reconstruction methods. It includes generation of random samples from a statistically described ensemble of 3D images resembling those to which PET would be applied in a medical situation, generation of corresponding projection data with noise and detector point spread function simulating those of a 3D PET scanner, assignment of figures of merit appropriate for the intended medical applications, optimization of the reconstruction algorithms on a training set of data, and statistical testing of the validity of hypotheses that say that two reconstruction algorithms perform equally well (from the point of view of a particular figure of merit) as compared to the alternative hypotheses that say that one of the algorithms outperforms the other. Although the methodology was developed with the 3D PET in mind, it can be used, with minor changes, for other 3D data collection methods, such as fully 3D cr or SPECT.

Algorithms↗
PubMed1994

Evaluation of task-oriented performance of several fully 3D PET reconstruction algorithms.

The relative performance of five fully 3D PET reconstruction algorithms is evaluated. The algorithms are a filtered backprojection (FBP) method and two variants each of the EM-ML and ART iterative methods. For each of the iterative methods, one variant makes use of voxels and the other makes use of 'blobs' (spherically symmetric functions smoothly decaying to zero at their boundaries) as basis functions in its discrete reconstruction model. The methods are evaluated from the point of view of the efficacy of the reconstructions produced by them for three typical medical tasks--estimation of the average activity inside specific regions of interest, detection of hot spots, and detection of cold spots. A free parameter is allowed in the description of each of the five algorithms; the parameters are determined by a training process during which a value of the free parameter is selected which (nearly) maximizes a technical figure of merit. Such training and the actual comparative evaluation is done by making use of randomly generated phantoms and their projection data. The methodology allows assignation of levels of statistical significance to claims of the relative superiority of one algorithm over another for a particular task. We find that using blobs as basis functions in the iterative algorithms is definitely advantageous over using voxels. This result has high statistical significance. (We also include a visual illustration of it.) Comparing FBP, EM-ML using blobs, and ART using blobs, we do not find a clear difference in the overall performance of the investigated variants of the methods. If anything, our results suggest that ART using blobs may be the most efficacious of the three.

Algorithms↗
PubMed1992

Fully three-dimensional reconstruction from data collected on concentric cubes in Fourier space: implementation and a sample application to MRI.

An algorithm is proposed for rapid and accurate reconstruction from data collected in Fourier space at points arranged on a grid of concentric cubes. The Fourier transform of the object to be reconstructed is decomposed into the sum of three functions by subdividing its domain into three non-overlapping mutually orthogonal double pyramids. Each of the three functions is zero-valued outside one of the double pyramids and has values inside that double pyramid which are the same as those of Fourier transform of the object to be reconstructed at the same points. Inverse Fourier transforms of these individual functions can be calculated using the chirp z-transform. The outputs of these inverse transforms for the three functions are estimates of their values at points of the same rectangular grid. The function to be reconstructed is estimated for this grid by adding together the three inverse transforms. The whole process has computational complexity of the same order as required for the 3D fast Fourier transform and so (for medically relevant sizes of the data set) it is faster than backprojection into the same size rectangular grid. The design of the algorithm ensures that no interpolations are needed, in contrast to methods involving backprojection with their unavoidable interpolations. As an application, a 3D data collection method for MRI has been designed which directly samples the Fourier transform of the object to be reconstructed on concentric cubes as needed for the algorithm.

Algorithms↗
PubMed1991

Analysis of brain and cerebrospinal fluid volumes with MR imaging. Part I. Methods, reliability, and validation.

A computerized system was developed to process standard spin-echo magnetic resonance (MR) imaging data for estimation of brain parenchyma and cerebrospinal fluid (CSF) volumes. In phantom experiments, the estimated volumes corresponded closely to the true volumes (r = .998), with a mean error less than 1.0 cm3 (for phantom volumes ranging from 5 to 35 cm3), with excellent intra- and interobserver reliability. In a clinical validation study with actual brain images of 10 human subjects, the average coefficient of variation between observers for the measurement of absolute brain and CSF volumes was 1.2% and 6.4%, respectively. The intraclass correlations for three expert operators is greater than .99 in the measurement of brain and ventricular volumes and greater than .94 for total CSF volume. Therefore, the authors believe that their technique to analyze MR images of the brain performed with acceptable levels of accuracy and reliability and that it can be used to measure brain and CSF volumes for clinical research. This technique could be helpful in the correlation of neuroanatomic measurements to behavioral and physiologic parameters in neuropsychiatric disorders.

Algorithms↗
PubMed1990

Two- and three-dimensional image reconstructions from stained and autoradiographed histological sections.

A complete system has been developed to utilize histological serial sections for two- and three-dimensional image reconstructions. Eighty to 120 sections are digitized using a personal computing system augmented with a imaging board and CCD camera. The image files are transmitted to a VAX computer for processing and image reconstruction, and the processed images are transmitted back to the personal computer for display and recording using a film recorder or PostScript printer. The software developed for the system allows serial sections to be placed into proper registration in a 256(3) array, 256 grey levels. Autoradiographs of the sections are obtained in the presence of appropriate standards which are used to recalibrate grey levels to represent linearly the radioactivity of each pixel in the sections and scale the values to allow maximum use of the grey scale. Starting from coronally sectioned material the system has been used to analyse and reconstruct rat nasal turbinates. In two dimensions horizontal and sagittal sections have been obtained while in three dimensions back-to-front and surface-rendered images have been constructed. Useful rendering of differential metabolic activity within an organ of complex geometry has been obtained, and there appears to be no reason why the system cannot be used for any material for which serial sectioning is appropriate.

Animals↗
PubMed1988

Three-dimensional imaging in medicine. A response to a critique by surgeons.

In a recent article in this Journal (Vol. 20:1) two surgeons gave a critique in which they discussed the relative merits and disadvantages of three-dimensional presentation based on CT scan data. While most of their critique is unarguable, there are some aspects of it which are overstated and possibly misleading. This is a response of a computer scientist, which attempts to present the somewhat different perception of one who is involved in the development of the three-dimensional imaging methodology in medicine.

Cost-Benefit Analysis↗
PubMed1987

Three-dimensional computed tomographic imaging.

Recent developments in imaging techniques now allow reconstruction of actual three-dimensional images from computed tomographic data. This article discusses the basic concepts involved in three-dimensional imaging and reviews its potential as a diagnostic and management tool for the clinical ophthalmologist. New computer techniques allow review of actual three-dimensional images in both static and dynamic formats. This can allow the clinician to define more accurately a normal and pathologic anatomy involving skeletal structures in particular.

Eye Diseases↗
PubMed1986

Three-dimensional computed tomography in maxillofacial trauma.

Roentgenographic evaluation of maxillofacial trauma is an integral component in the management of the acutely injured patient. Recent developments in computerized software permit three-dimensional computed tomographic (CT) reconstructions of complex anatomic parts. Five examples of complex maxillofacial trauma were demonstrated by conventional plain films, followed by two-dimensional and three-dimensional CT. Three-dimensional CT vividly demonstrates spatial relationships not easily conceptualized by present modalities.

Adult↗
PubMed1986

Acetabular fractures: three-dimensional computer tomographic imaging and interactive surgical planning.

Three-dimensional imaging can provide a valuable perceptual link between conventional radiographs and axial computed tomographic scans in the evaluation of complex acetabular fractures. With the 3D83 computer program, three-dimensional images can be generated to correlate with standard radiographic views. Unique images can also be created that offer perspectives unobtainable by conventional radiography. More sophisticated interactive techniques allow computer simulation of surgical approaches.

Acetabulum↗