Automated electron microscope tomography using robust prediction of specimen movements

A new method was developed to acquire images automatically at a series of specimen tilts, as required for tomographic reconstruction. The method uses changes in specimen position at previous tilt angles to predict the position at the current tilt angle. Actual measurement of the position or focus is skipped if the statistical error of the prediction is low enough. This method allows a tilt series to be acquired rapidly when conditions are good but falls back toward the traditional approach of taking focusing and tracking images when necessary. The method has been implemented in a program, SerialEM, that provides an efficient environment for data acquisition. This program includes control of an energy filter as well as a low-dose imaging mode, in which tracking and focusing occur away from the area of interest. The program can automatically acquire a montage of overlapping frames, allowing tomography of areas larger than the field of the CCD camera. It also includes tools for navigating between specimen positions and finding regions of interest.

Photoacoustic tomography: in vivo imaging from organelles to organs

Photoacoustic tomography (PAT) can create multiscale multicontrast images of living biological structures ranging from organelles to organs. This emerging technology overcomes the high degree of scattering of optical photons in biological tissue by making use of the photoacoustic effect. Light absorption by molecules creates a thermally induced pressure jump that launches ultrasonic waves, which are received by acoustic detectors to form images. Different implementations of PAT allow the spatial resolution to be scaled with the desired imaging depth in tissue while a high depth-to-resolution ratio is maintained. As a rule of thumb, the achievable spatial resolution is on the order of 1/200 of the desired imaging depth, which can reach up to 7 centimeters. PAT provides anatomical, functional, metabolic, molecular, and genetic contrasts of vasculature, hemodynamics, oxygen metabolism, biomarkers, and gene expression. We review the state of the art of PAT for both biological and clinical studies and discuss future prospects.

Low resolution electromagnetic tomography: a new method for localizing electrical activity in the brain

This paper presents a new method for localizing the electric activity in the brain based on multichannel surface EEG recordings. In contrast to the models presented up to now the new method does not assume a limited number of dipolar point sources nor a distribution on a given known surface, but directly computes a current distribution throughout the full brain volume. In order to find a unique solution for the 3-dimensional distribution among the infinite set of different possible solutions, the method assumes that neighboring neurons are simultaneously and synchronously activated. The basic assumption rests on evidence from single cell recordings in the brain that demonstrates strong synchronization of adjacent neurons. In view of this physiological consideration the computational task is to select the smoothest of all possible 3-dimensional current distributions, a task that is a common procedure in generalized signal processing. The result is a true 3-dimensional tomography with the characteristic that localization is preserved with a certain amount of dispersion, i.e., it has a relatively low spatial resolution. The new method, which we call Low Resolution Electromagnetic Tomography (LORETA) is illustrated with two different sets of evoked potential data, the first showing the tomography of the P100 component to checkerboard stimulation of the left, right, upper and lower hemiretina, and the second showing the results for the auditory N100 component and the two cognitive components CNV and P300. A direct comparison of the tomography results with those obtained from fitting one and two dipoles illustrates that the new method provides physiologically meaningful results while dipolar solutions fail in many situations. In the case of the cognitive components, the method offers new hypotheses on the location of higher cognitive functions in the brain.

Characterization of human atherosclerosis by optical coherence tomography

BACKGROUND

High-resolution visualization of atherosclerotic plaque morphology may be essential for identifying coronary plaques that cause acute coronary events. Optical coherence tomography (OCT) is an intravascular imaging modality capable of providing cross-sectional images of tissue with a resolution of 10 micro m. To date, OCT imaging has not been investigated in sufficient detail to assess its accuracy for characterizing atherosclerotic plaques. The aim of this study was to establish objective OCT image criteria for atherosclerotic plaque characterization in vitro.

METHODS AND RESULTS

OCT images of 357 (diseased) atherosclerotic arterial segments obtained at autopsy were correlated with histology. OCT image criteria for 3 types of plaque were formulated by analysis of a subset (n=50) of arterial segments. OCT images of fibrous plaques were characterized by homogeneous, signal-rich regions; fibrocalcific plaques by well-delineated, signal-poor regions with sharp borders; and lipid-rich plaques by signal-poor regions with diffuse borders. Independent validation of these criteria by 2 OCT readers for the remaining segments (n=307) demonstrated a sensitivity and specificity ranging from 71% to 79% and 97% to 98% for fibrous plaques, 95% to 96% and 97% for fibrocalcific plaques, and 90% to 94% and 90% to 92% for lipid-rich plaques, respectively (overall agreement, kappa=0.83 to 0.84). The interobserver and intraobserver reliabilities of OCT assessment were high (kappa values of 0.88 and 0.91, respectively).

CONCLUSIONS

Objective OCT criteria are highly sensitive and specific for characterizing different types of atherosclerotic plaques. These results represent an important step in validating this new intravascular imaging modality and will provide a basis for the interpretation of intracoronary OCT images obtained from patients.

Tomographic imaging using the nonlinear response of magnetic particles

The use of contrast agents and tracers in medical imaging has a long history. They provide important information for diagnosis and therapy, but for some desired applications, a higher resolution is required than can be obtained using the currently available medical imaging techniques. Consider, for example, the use of magnetic tracers in magnetic resonance imaging: detection thresholds for in vitro and in vivo imaging are such that the background signal from the host tissue is a crucial limiting factor. A sensitive method for detecting the magnetic particles directly is to measure their magnetic fields using relaxometry; but this approach has the drawback that the inverse problem (associated with transforming the data into a spatial image) is ill posed and therefore yields low spatial resolution. Here we present a method for obtaining a high-resolution image of such tracers that takes advantage of the nonlinear magnetization curve of small magnetic particles. Initial 'phantom' experiments are reported that demonstrate the feasibility of the imaging method. The resolution that we achieve is already well below 1 mm. We evaluate the prospects for further improvement, and show that the method has the potential to be developed into an imaging method characterized by both high spatial resolution as well as high sensitivity.

Imaging of macular diseases with optical coherence tomography

BACKGROUND/PURPOSE

To assess the potential of a new diagnostic technique called optical coherence tomography for imaging macular disease. Optical coherence tomography is a novel noninvasive, noncontact imaging modality which produces high depth resolution (10 microns) cross-sectional tomographs of ocular tissue. It is analogous to ultrasound, except that optical rather than acoustic reflectivity is measured.

METHODS

Optical coherence tomography images of the macula were obtained in 51 eyes of 44 patients with selected macular diseases. Imaging is performed in a manner compatible with slit-lamp indirect biomicroscopy so that high-resolution optical tomography may be accomplished simultaneously with normal ophthalmic examination. The time-of-flight delay of light backscattered from different layers in the retina is determined using low-coherence interferometry. Cross-sectional tomographs of the retina profiling optical reflectivity versus distance into the tissue are obtained in 2.5 seconds and with a longitudinal resolution of 10 microns.

RESULTS

Correlation of fundus examination and fluorescein angiography with optical coherence tomography tomographs was demonstrated in 12 eyes with the following pathologies: full- and partial-thickness macular hole, epiretinal membrane, macular edema, intraretinal exudate, idiopathic central serous chorioretinopathy, and detachments of the pigment epithelium and neurosensory retina.

CONCLUSION

Optical coherence tomography is potentially a powerful tool for detecting and monitoring a variety of macular diseases, including macular edema, macular holes, and detachments of the neurosensory retina and pigment epithelium.

In vivo endoscopic optical biopsy with optical coherence tomography

Current medical imaging technologies allow visualization of tissue anatomy in the human body at resolutions ranging from 100 micrometers to 1 millimeter. These technologies are generally not sensitive enough to detect early-stage tissue abnormalities associated with diseases such as cancer and atherosclerosis, which require micrometer-scale resolution. Here, optical coherence tomography was adapted to allow high-speed visualization of tissue in a living animal with a catheter-endoscope 1 millimeter in diameter. This method, referred to as "optical biopsy," was used to obtain cross-sectional images of the rabbit gastrointestinal and respiratory tracts at 10-micrometer resolution.

Visualization of coronary atherosclerotic plaques in patients using optical coherence tomography: comparison with intravascular ultrasound

OBJECTIVES

The aim of this study was to evaluate the feasibility and the ability of intravascular optical coherence tomography (OCT) to visualize the components of coronary plaques in living patients.

BACKGROUND

Disruption of a vulnerable coronary plaque with subsequent thrombosis is currently recognized as the primary mechanism for acute myocardial infarction. Although such plaques are considered to have a thin fibrous cap overlying a lipid pool, imaging modalities in current clinical practice do not have sufficient resolution to identify thin (< 65 microm) fibrous caps. Optical coherence tomography is a new imaging modality capable of obtaining cross-sectional images of coronary vessels at a resolution of approximately 10 microm.

METHODS

The OCT images and corresponding histology of 42 coronary plaques were compared to establish OCT criteria for different types of plaques. Atherosclerotic lesions with mild to moderate stenosis were identified on angiograms in 10 patients undergoing cardiac catheterization. Optical coherence tomography and intravascular ultrasound (IVUS) images of these sites were obtained in all patients without complication.

RESULTS

Comparison between OCT and histology demonstrated that lipid-rich plaques and fibrous plaques have distinct OCT characteristics. A total of 17 IVUS and OCT image pairs obtained from patients were compared. Axial resolution measured 13 +/- 3 microm with OCT and 98 +/- 19 microm with IVUS. All fibrous plaques, macrocalcifications and echolucent regions identified by IVUS were visualized in corresponding OCT images. Intimal hyperplasia and echolucent regions, which may correspond to lipid pools, were identified more frequently by OCT than by IVUS.

CONCLUSIONS

Intracoronary OCT appears to be feasible and safe. Optical coherence tomography identified most architectural features detected by IVUS and may provide additional detailed structural information.

Optical coherence tomography: an emerging technology for biomedical imaging and optical biopsy

Optical coherence tomography (OCT) is an emerging technology for performing high-resolution cross-sectional imaging. OCT is analogous to ultrasound imaging, except that it uses light instead of sound. OCT can provide cross-sectional images of tissue structure on the micron scale in situ and in real time. Using OCT in combination with catheters and endoscopes enables high-resolution intraluminal imaging of organ systems. OCT can function as a type of optical biopsy and is a powerful imaging technology for medical diagnostics because unlike conventional histopathology which requires removal of a tissue specimen and processing for microscopic examination, OCT can provide images of tissue in situ and in real time. OCT can be used where standard excisional biopsy is hazardous or impossible, to reduce sampling errors associated with excisional biopsy, and to guide interventional procedures. In this paper, we review OCT technology and describe its potential biomedical and clinical applications.

Concurrent MRI and diffuse optical tomography of breast after indocyanine green enhancement

We present quantitative optical images of human breast in vivo. The images were obtained by using near-infrared diffuse optical tomography (DOT) after the administration of indocyanine green (ICG) for contrast enhancement. The optical examination was performed concurrently with a magnetic resonance imaging (MRI) exam on patients scheduled for excisional biopsy or surgery so that accurate image coregistration and histopathological information of the suspicious lesions was available. The ICG-enhanced optical images coregistered accurately with Gadolinium-enhanced magnetic resonance images validating the ability of DOT to image breast tissue. In contrast to simple transillumination, we found that DOT provides for localization and quantification of exogenous tissue chromophore concentrations. Additionally our use of ICG, an albumin bound absorbing dye in plasma, demonstrates the potential to differentiate disease based on the quantified enhancement of suspicious lesions.

Tomographic phase microscopy

We report a technique for quantitative three-dimensional (3D) mapping of refractive index in live cells and tissues using a phase-shifting laser interferometric microscope with variable illumination angle. We demonstrate tomographic imaging of cells and multicellular organisms, and time-dependent changes in cell structure. Our results will permit quantitative characterization of specimen-induced aberrations in high-resolution microscopy and have multiple applications in tissue light scattering.

In vivo human retinal imaging by Fourier domain optical coherence tomography

We present what is to our knowledge the first in vivo tomograms of human retina obtained by Fourier domain optical coherence tomography. We would like to show that this technique might be as powerful as other optical coherence tomography techniques in the ophthalmologic imaging field. The method, experimental setup, data processing, and images are discussed.

Optical biopsy and imaging using optical coherence tomography

Optical coherence tomography is a new imaging technique that can perform high-resolution, micrometre-scale, cross-sectional imaging in biological systems. The technology has been developed, and reduced to, preliminary clinical practice in ophthalmology. The challenging problem that OCT may address is the development of 'optical biopsy' techniques. These techniques can provide diagnostic imaging of tissue morphology without the need for excision of specimens. Many investigations remain to identify optimal areas for clinical application, and additional engineering must be done to integrate vertically the technology and to reduce it to clinical practice. Nevertheless, preliminary studies indicate the feasibility of developing this technology for a wide range of clinical and research diagnostic imaging applications. The ability to non-excisionally evaluate tissue morphology using a catheter or an endoscope could have a significant impact on the diagnosis and management of a wide range of diseases.

TOM software toolbox: acquisition and analysis for electron tomography

Automated data acquisition procedures have changed the perspectives of electron tomography (ET) in a profound manner. Elaborate data acquisition schemes with autotuning functions minimize exposure of the specimen to the electron beam and sophisticated image analysis routines retrieve a maximum of information from noisy data sets. "TOM software toolbox" integrates established algorithms and new concepts tailored to the special needs of low dose ET. It provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis. Designed as a collection of computational procedures it is a complete software solution within a highly flexible framework. TOM represents a new way of working with the electron microscope and can serve as the basis for future high-throughput applications.

Optical coherence tomography of macular holes

PURPOSE

To assess the potential of a new diagnostic technique called optical coherence tomography (OCT) for diagnosing and monitoring macular holes. This technique is a novel noninvasive, noncontact imaging modality that produces high longitudinal resolution (10-micron) cross-sectional tomographs of ocular tissue.

METHODS

Optical coherence tomography is analogous to ultrasound except that optical rather than acoustic reflectivity is measured. Cross-sectional tomographs of the retina profiling optical reflectivity in a thin, optical slice of tissue are obtained with a longitudinal resolution of 10 microns. Optical coherence tomography was used to examine 49 patients with the clinical diagnosis of idiopathic full-thickness macular hole, impending macular hole, epimacular membrane with macular pseudohole, or partial-thickness hole. The resulting OCTs were correlated with contact lens and slit-lamp biomicroscopy, fundus photography, and fluorescein angiography.

RESULTS

The cross-sectional view produced by OCT was effective in distinguishing full-thickness macular holes from partial-thickness holes, macular pseudoholes, and cysts. Optical coherence tomography was successful in staging macular holes and provided a quantitative measure of hole diameter and the amount of surrounding macular edema. Optical coherence tomography also was used to evaluate the vitreoretinal interface in patients' fellow eyes and was able to detect small separations of the posterior hyaloid from the retina.

CONCLUSION

Optical coherence tomography appears potentially useful as a new, noninvasive, diagnostic technique for visualizing and quantitatively characterizing macular holes and assessing fellow eyes of patients with a macular hole. The tomographic information provided by OCT eventually may lead to a better understanding of the pathogenesis of macular hole formation.

Optical coherence tomography in dermatology: a review

BACKGROUND/AIMS

Optical coherence tomography (OCT) is a non-invasive technique for morphological investigation of tissue. Since its development in the late 1980s it is mainly used as a diagnostic tool in ophthalmology. For examination of a highly scattering tissue like the skin, it was necessary to modify the method. Early studies on the value of OCT for skin diagnosis gave promising results.

METHODS

The OCT technique is based on the principle of Michelson interferometry. The light sources used for OCT are low coherent superluminescent diodes operating at a wavelength of about 1300 nm. OCT provides two-dimensional images with a scan length of a few millimeters (mm), a resolution of about 15 microns and a maximum detection depth of 1.5 mm. The image acquisition can be performed nearly in real time. The measurement is non-invasive and with no side effects.

RESULTS

The in vivo OCT images of human skin show a strong scattering from tissue with a few layers and some optical inhomogeneities. The resolution enables the visualization of architectural changes, but not of single cells. In palmoplantar skin, the thick stratum comeum is visible as a low-scattering superficial well defined layer with spiral sweat gland ducts inside. The epidermis can be distinguished from the dermis. Adnexal structures and blood vessels are low-scattering regions in the upper dermis. Skin tumors show a homogenous signal distribution. In some cases, tumor borders to healthy skin are detectable. Inflammatory skin diseases lead to changes of the OCT image, such as thickening of the epidermis and reduction of the light attenuation in the dermis. A quantification of treatment effects, such as swelling of the horny layer due to application of a moisturizer, is possible. Repeated measurements allow a monitoring of the changes over time.

CONCLUSION

OCT is a promising new bioengineering method for investigation of skin morphology. In some cases it may be useful for diagnosis of skin diseases. Because of its non-invasive character, the technique allows monitoring of inflammatory diseases over time. An objective quantification of the efficacy and tolerance of topical treatment is also possible. Due to the high resolution and simple application, OCT is an interesting addition to other morphological techniques in dermatology.

A positron-emission transaxial tomograph for nuclear imaging (PETT)

An apparatus was developed for obtaining emission transaxial images of sections of organs containing positron-emitting radiopharmaceuticals. The detection system is a hexagonal array of 24 NaI(T1) detectors connected to coincidence circuits to achieve the "electronic" collimation of annihilation photons. The image is formed by a computer-applied algorithm which provides quantitative reconstruction of the distribution of activity. Computer simulations, phantom and animal studies show that this approach is capable of providing images of better contrast and resolution than are obtained with scintillation cameras. Advantages of positron vs. single photon reconstruction tomography are discussed.

Histopathologic validation of Fourier-ellipsometry measurements of retinal nerve fiber layer thickness

We describe a new technique for the measurement of retinal nerve fiber layer thickness and compare its results with histopathologic measurements in the same eyes. For these studies, two fixed monkey eyes were incised and placed on a pedestal in a plastic viewing dish. The eyes were perfused to maintain a pressure between 10 and 20 mm Hg. An ellipsometer, an optical device used to measure the change in polarization of light (retardation), was implemented in a laser tomographic scanner to obtain polarization data from the two monkey retinas. For the 15 measured locations, retardation ranged between a mean (+/- SD) of 0.9 degrees +/- 1.8 degrees and 23.7 degrees +/- 0.3 degrees. Subsequently, retinal nerve fiber layer thickness was measured at the imaged points in epoxy resin-embedded sections by an observer masked to the ellipsometry data. These values ranged between 20.4 microns and 213.9 microns. There was an excellent correlation (R = .83) between retardation and the histopathologic measurement of retinal nerve fiber layer thickness. Quantitating retinal nerve fiber layer thickness may enhance discrimination between glaucomatous and normal eyes earlier than is currently available by anatomic and functional approaches.

Quantitative hemoglobin tomography with diffuse near-infrared spectroscopy: pilot results in the breast

The authors describe what is, to the best of their knowledge, the first quantitative hemoglobin concentration images of the female breast that were formed with model-based reconstruction of near-infrared intensity-modulated tomographic data. The results in 11 patients, including two with breast tumors with pathologic correlation, are summarized. Hemoglobin concentration appears to correlate with tumor vascularity without the need for exogenous contrast material and thereby has intrinsic diagnostic value.

High-resolution full-field optical coherence tomography with a Linnik microscope

We describe an original microscope for high-resolution optical coherence tomography applications. Our system is based on a Linnik interference microscope with high-numerical-aperture objectives. Lock-in detection of the interference signal is achieved in parallel on a CCD by use of a photoelastic birefringence modulator and full-field stroboscopic illumination with an infrared LED. Transverse cross-section (en-face, or XY) images can be obtained in real time with better than 1-microm axial (Z) resolution and 0.5-microm transverse (XY) resolution. A sensitivity of approximately 80 dB is reached at a 1-image/s acquisition rate, which allows tomography in scattering media such as biological tissues.

Fluorescence-enhanced, near infrared diagnostic imaging with contrast agents

The deep tissue propagation of near-infrared (NIR) light between 700-900 nm offers new opportunities for diagnostic imaging when employing sensitive detection techniques and NIR excitable fluorescent agents that target and report disease and metabolism. Herein, we highlight approaches for illuminating tissues and monitoring the re-emitted fluorescence for tomographic reconstruction, strategies for developing fluorescent dye constructs, and clinical opportunities for fluorescence-enhanced NIR optical imaging.

Electrical impedance tomography (EIT): a review

Electrical impedance tomography (EIT) has been the subject of quite intensive research for about 20 years but has yet to become established as a routine tool in healthcare. None the less the volume of published research work in this area is still rising. This review takes a broad look at what has been achieved and attempts to give the reader sufficient information to form an opinion as to the likely future for this interesting area of research.

High-resolution imaging of the human esophagus and stomach in vivo using optical coherence tomography

BACKGROUND

Optical coherence tomography is a new, high spatial-resolution, cross-sectional imaging technique. We investigated the ability of optical coherence tomography to provide detailed images of subsurface structures in the upper gastrointestinal (GI) tract.

METHODS

Optical coherence tomography was performed during routine upper GI endoscopy on 32 patients including 20 patients with Barrett's esophagus. An endoscopic mucosal biopsy was obtained immediately after imaging and was used for histopathologic correlation.

RESULTS

Optical coherence tomography provided clear delineation of layers of the normal human esophagus extending from the epithelium to the longitudinal muscularis propria. Gastric mucosa was differentiated from esophageal mucosa, Barrett's esophagus was differentiated from normal esophageal mucosa, and esophageal adenocarcinoma was distinguished from normal esophagus and Barrett's esophagus.

CONCLUSIONS

Optical coherence tomography allows visualization of the subsurface architectural morphology of the upper GI tract. The diagnostic information provided by this new imaging modality suggests that it may be a useful adjunct to endoscopy.

Developments toward diagnostic breast cancer imaging using near-infrared optical measurements and fluorescent contrast agents

The use of near-infrared (NIR) light to interrogate deep tissues has enormous potential for molecular-based imaging when coupled with NIR excitable dyes. More than a decade has now passed since the initial proposals for NIR optical tomography for breast cancer screening using time-dependent measurements of light propagation in the breast. Much accomplishment in the development of optical mammography has been demonstrated, most recently in the application of time-domain, frequency-domain, and continuous-wave measurements that depend on endogenous contrast owing to angiogenesis and increased hemoglobin absorbance for contrast. Although exciting and promising, the necessity of angiogenesis-mediated absorption contrast for diagnostic optical mammography minimizes the potential for using NIR techniques to assess sentinel lymph node staging, metastatic spread, and multifocality of breast disease, among other applications. In this review, we summarize the progress made in the development of optical mammography, and focus on the emerging work underway in the use of diagnostic contrast agents for the molecular-based, diagnostic imaging of breast.