In this study we present a computational method of CT examination classification into visual assessed
emphysema severity. The visual severity categories ranged from 0 to 5 and were rated by an experienced
radiologist. The six categories were none, trace, mild, moderate, severe and very severe. Lung segmentation
was performed for every input image and all image features are extracted from the segmented lung only. We
adopted a two-level feature representation method for the classification. Five gray level distribution statistics,
six gray level co-occurrence matrix (GLCM), and eleven gray level run-length (GLRL) features were
computed for each CT image depicted segment lung. Then we used wavelets decomposition to obtain the
low- and high-frequency components of the input image, and again extract from the lung region six GLCM
features and eleven GLRL features. Therefore our feature vector length is 56. The CT examinations were
classified using the support vector machine (SVM) and k-nearest neighbors (KNN) and the traditional
threshold (density mask) approach. The SVM classifier had the highest classification performance of all the
methods with an overall sensitivity of 54.4% and a 69.6% sensitivity to discriminate "no" and "trace visually
assessed emphysema. We believe this work may lead to an automated, objective method to categorically
classify emphysema severity on CT exam.
We developed a new pulmonary vascular tree segmentation/extraction algorithm. The purpose of this study was to
assess whether adding this new algorithm to our previously developed computer-aided detection (CAD) scheme of
pulmonary embolism (PE) could improve the CAD performance (in particular reducing false positive detection rates). A
dataset containing 12 CT examinations with 384 verified pulmonary embolism regions associated with 24 threedimensional
(3-D) PE lesions was selected in this study. Our new CAD scheme includes the following image processing
and feature classification steps. (1) A 3-D based region growing process followed by a rolling-ball algorithm was
utilized to segment lung areas. (2) The complete pulmonary vascular trees were extracted by combining two approaches
of using an intensity-based region growing to extract the larger vessels and a vessel enhancement filtering to extract the
smaller vessel structures. (3) A toboggan algorithm was implemented to identify suspicious PE candidates in segmented
lung or vessel area. (4) A three layer artificial neural network (ANN) with the topology 27-10-1 was developed to reduce
false positive detections. (5) A k-nearest neighbor (KNN) classifier optimized by a genetic algorithm was used to
compute detection scores for the PE candidates. (6) A grouping scoring method was designed to detect the final PE
lesions in three dimensions. The study showed that integrating the pulmonary vascular tree extraction algorithm into the
CAD scheme reduced false positive rates by 16.2%. For the case based 3D PE lesion detecting results, the integrated
CAD scheme achieved 62.5% detection sensitivity with 17.1 false-positive lesions per examination.
Bilateral mammographic tissue density asymmetry could be an important factor in assessing risk of developing
breast cancer and improving the detection of the suspicious lesions. This study aims to assess whether fusion of the
bilateral mammographic density asymmetrical information into a computer-aided detection (CAD) scheme could
improve CAD performance in detecting mass-like breast cancers. A testing dataset involving 1352 full-field digital
mammograms (FFDM) acquired from 338 cases was used. In this dataset, half (169) cases are positive containing
malignant masses and half are negative. Two computerized schemes were first independently applied to process FFDM
images of each case. The first single-image based CAD scheme detected suspicious mass regions on each image. The
second scheme detected and computed the bilateral mammographic tissue density asymmetry for each case. A fusion
method was then applied to combine the output scores of the two schemes. The CAD performance levels using the
original CAD-generated detection scores and the new fusion scores were evaluated and compared using a free-response
receiver operating characteristic (FROC) type data analysis method. By fusion with the bilateral mammographic density
asymmetrical scores, the case-based CAD sensitivity was increased from 79.2% to 84.6% at a false-positive rate of 0.3
per image. CAD also cued more "difficult" masses with lower CAD-generated detection scores while discarded some
"easy" cases. The study indicated that fusion between the scores generated by a single-image based CAD scheme and the
computed bilateral mammographic density asymmetry scores enabled to increase mass detection sensitivity in particular
to detect more subtle masses.
Fluorescence in situ hybridization (FISH) technology provides a promising molecular imaging tool to detect cervical
cancer. Since manual FISH analysis is difficult, time-consuming, and inconsistent, the automated FISH image scanning
systems have been developed. Due to limited focal depth of scanned microscopic image, a FISH-probed specimen needs
to be scanned in multiple layers that generate huge image data. To improve diagnostic efficiency of using automated
FISH image analysis, we developed a computer-aided detection (CAD) scheme. In this experiment, four pap-smear
specimen slides were scanned by a dual-detector fluorescence image scanning system that acquired two spectrum images
simultaneously, which represent images of interphase cells and FISH-probed chromosome X. During image scanning,
once detecting a cell signal, system captured nine image slides by automatically adjusting optical focus. Based on the
sharpness index and maximum intensity measurement, cells and FISH signals distributed in 3-D space were projected
into a 2-D con-focal image. CAD scheme was applied to each con-focal image to detect analyzable interphase cells using
an adaptive multiple-threshold algorithm and detect FISH-probed signals using a top-hat transform. The ratio of
abnormal cells was calculated to detect positive cases. In four scanned specimen slides, CAD generated 1676 con-focal
images that depicted analyzable cells. FISH-probed signals were independently detected by our CAD algorithm and an
observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in
detecting/counting FISH signal spots. The study demonstrated the feasibility of applying automated FISH image and
signal analysis to assist cyto-geneticists in detecting cervical cancers.
In order to establish a personalized breast cancer screening program, it is important to develop risk models that have
high discriminatory power in predicting the likelihood of a woman developing an imaging detectable breast cancer in
near-term (e.g., <3 years after a negative examination in question). In epidemiology-based breast cancer risk models,
mammographic density is considered the second highest breast cancer risk factor (second to woman's age). In this study
we explored a new feature, namely bilateral mammographic density asymmetry, and investigated the feasibility of
predicting near-term screening outcome. The database consisted of 343 negative examinations, of which 187 depicted
cancers that were detected during the subsequent screening examination and 155 that remained negative. We computed
the average pixel value of the segmented breast areas depicted on each cranio-caudal view of the initial negative
examinations. We then computed the mean and difference mammographic density for paired bilateral images. Using
woman's age, subjectively rated density (BIRADS), and computed mammographic density related features we compared
classification performance in estimating the likelihood of detecting cancer during the subsequent examination using
areas under the ROC curves (AUC). The AUCs were 0.63±0.03, 0.54±0.04, 0.57±0.03, 0.68±0.03 when using woman's
age, BIRADS rating, computed mean density and difference in computed bilateral mammographic density, respectively.
Performance increased to 0.62±0.03 and 0.72±0.03 when we fused mean and difference in density with woman's age.
The results suggest that, in this study, bilateral mammographic tissue density is a significantly stronger (p<0.01) risk
indicator than both woman's age and mean breast density.
In this study we present a texture-based method of emphysema segmentation depicted on CT examination consisting of
two steps. Step 1, a fractal dimension based texture feature extraction is used to initially detect base regions of
emphysema. A threshold is applied to the texture result image to obtain initial base regions. Step 2, the base regions are
evaluated pixel-by-pixel using a method that considers the variance change incurred by adding a pixel to the base in an
effort to refine the boundary of the base regions. Visual inspection revealed a reasonable segmentation of the emphysema
regions. There was a strong correlation between lung function (FEV1%, FEV1/FVC, and DLCO%) and fraction of
emphysema computed using the texture based method, which were -0.433, -.629, and -0.527, respectively. The texture-based
method produced more homogeneous emphysematous regions compared to simple thresholding, especially for
large bulla, which can appear as speckled regions in the threshold approach. In the texture-based method, single isolated
pixels may be considered as emphysema only if neighboring pixels meet certain criteria, which support the idea that
single isolated pixels may not be sufficient evidence that emphysema is present. One of the strength of our complex
texture-based approach to emphysema segmentation is that it goes beyond existing approaches that typically extract a
single or groups texture features and individually analyze the features. We focus on first identifying potential regions of
emphysema and then refining the boundary of the detected regions based on texture patterns.
We have developed a multi-probe resonance-frequency electrical impedance spectroscope (REIS) system to detect breast
abnormalities. Based on assessing asymmetry in REIS signals acquired between left and right breasts, we developed
several machine learning classifiers to classify younger women (i.e., under 50YO) into two groups of having high and
low risk for developing breast cancer. In this study, we investigated a new method to optimize performance based on the
area under a selected partial receiver operating characteristic (ROC) curve when optimizing an artificial neural network
(ANN), and tested whether it could improve classification performance. From an ongoing prospective study, we selected
a dataset of 174 cases for whom we have both REIS signals and diagnostic status verification. The dataset includes 66
"positive" cases recommended for biopsy due to detection of highly suspicious breast lesions and 108 "negative" cases
determined by imaging based examinations. A set of REIS-based feature differences, extracted from the two breasts
using a mirror-matched approach, was computed and constituted an initial feature pool. Using a leave-one-case-out
cross-validation method, we applied a genetic algorithm (GA) to train the ANN with an optimal subset of features. Two
optimization criteria were separately used in GA optimization, namely the area under the entire ROC curve (AUC) and
the partial area under the ROC curve, up to a predetermined threshold (i.e., 90% specificity). The results showed that
although the ANN optimized using the entire AUC yielded higher overall performance (AUC = 0.83 versus 0.76), the
ANN optimized using the partial ROC area criterion achieved substantially higher operational performance (i.e.,
increasing sensitivity level from 28% to 48% at 95% specificity and/ or from 48% to 58% at 90% specificity).
We have developed and preliminarily tested a new breast cancer risk prediction model based on computerized
bilateral mammographic tissue asymmetry. In this study, we investigated and compared the performance difference of
our risk prediction model when the bilateral mammographic tissue asymmetrical features were extracted in two different
methods namely (1) the entire breast area and (2) the mirror-matched local strips between the left and right breast. A
testing dataset including bilateral craniocaudal (CC) view images of 100 negative and 100 positive cases for developing
breast abnormalities or cancer was selected from a large and diverse full-field digital mammography (FFDM) image
database. To detect bilateral mammographic tissue asymmetry, a set of 20 initial "global" features were extracted from
the entire breast areas of two bilateral mammograms in CC view and their differences were computed. Meanwhile, a
pool of 16 local histogram-based statistic features was computed from eight mirror-matched strips between the left and
right breast. Using a genetic algorithm (GA) to select optimal features, two artificial neural networks (ANN) were built
to predict the risk of a test case developing cancer. Using the leave-one-case-out training and testing method, two GAoptimized
ANNs yielded the areas under receiver operating characteristic (ROC) curves of 0.754±0.024 (using feature
differences extracted from the entire breast area) and 0.726±0.026 (using the feature differences extracted from 8 pairs of
local strips), respectively. The risk prediction model using either ANN is able to detect 58.3% (35/60) of cancer cases 6
to 18 months earlier at 80% specificity level. This study compared two methods to compute bilateral mammographic
tissue asymmetry and demonstrated that bilateral mammographic tissue asymmetry was a useful breast cancer risk
indicator with high discriminatory power.
After developing a multi-probe resonance-frequency electrical impedance spectroscopy (REIS) system aimed at
detecting women with breast abnormalities that may indicate a developing breast cancer, we have been conducting a
prospective clinical study to explore the feasibility of applying this REIS system to classify younger women (< 50 years
old) into two groups of "higher-than-average risk" and "average risk" of having or developing breast cancer. The system
comprises one central probe placed in contact with the nipple, and six additional probes uniformly distributed along an
outside circle to be placed in contact with six points on the outer breast skin surface. In this preliminary study, we
selected an initial set of 174 examinations on participants that have completed REIS examinations and have clinical
status verification. Among these, 66 examinations were recommended for biopsy due to findings of a highly suspicious
breast lesion ("positives"), and 108 were determined as negative during imaging based procedures ("negatives"). A set
of REIS-based features, extracted using a mirror-matched approach, was computed and fed into five machine learning
classifiers. A genetic algorithm was used to select an optimal subset of features for each of the five classifiers. Three
fusion rules, namely sum rule, weighted sum rule and weighted median rule, were used to combine the results of the
classifiers. Performance evaluation was performed using a leave-one-case-out cross-validation method. The results
indicated that REIS may provide a new technology to identify younger women with higher than average risk of having
or developing breast cancer. Furthermore, it was shown that fusion rule, such as a weighted median fusion rule and a
weighted sum fusion rule may improve performance as compared with the highest performing single classifier.
Visually searching for analyzable metaphase chromosome cells under microscopes is a routine and timeconsuming
task in genetic laboratories to diagnose cancer and genetic disorders. To improve detection efficiency,
consistency, and accuracy, we developed an automated microscopic image scanning system using a 100X oil immersion
objective lens to acquire images that has sufficient spatial resolution allowing clinicians to do diagnosis. Due to the highresolution,
the field of image depth is very limited and multiple scans up to seven layers are required. Thus, a metaphase
cell can spread over multiple images at different focal levels. Among them only one or two are adequate for the
diagnosis and the others are typically fuzzy images. In this study, we developed and tested a computer-aided detection
(CAD) scheme to automatically select one image with the sharpest image quality and discard all of the other fuzzy
images based on the computed sharpness index. From three scanned bone marrow specimen slides, the on-line and offline
metaphase finding modules automatically selected 100 chromosome cells with 534 images. These images were
selected to build a testing dataset. For each cell, the CAD scheme selects one image with the maximum sharpness index.
Three observers also independently visually selected one best image for diagnosis from each cell. The agreement rate
between CAD and visually selected images ranges from 89% to 96%, which is also very comparable to the agreement
rate between the two observers. This experiment demonstrated the feasibility of applying a CAD scheme to select the
images with sharpest high-resolution metaphase chromosome cell and potentially improve diagnostic efficiency and
accuracy in the future clinical practice.
Karyotyping is an important process to classify chromosomes into standard classes and the results are routinely used by the clinicians to diagnose cancers and genetic diseases. However, visual karyotyping using microscopic images is time-consuming and tedious, which reduces the diagnostic efficiency and accuracy. Although many efforts have been made to develop computerized schemes for automated karyotyping, no schemes can get be performed without substantial human intervention. Instead of developing a method to classify all chromosome classes, we develop an automatic scheme to detect abnormal metaphase cells by identifying a specific class of chromosomes (class 22) and prescreen for suspicious chronic myeloid leukemia (CML). The scheme includes three steps: (1) iteratively segment randomly distributed individual chromosomes, (2) process segmented chromosomes and compute image features to identify the candidates, and (3) apply an adaptive matching template to identify chromosomes of class 22. An image data set of 451 metaphase cells extracted from bone marrow specimens of 30 positive and 30 negative cases for CML is selected to test the scheme's performance. The overall case-based classification accuracy is 93.3% (100% sensitivity and 86.7% specificity). The results demonstrate the feasibility of applying an automated scheme to detect or prescreen the suspicious cancer cases.
Visually searching for analyzable metaphase chromosome cells under microscopes is quite time-consuming and
difficult. To improve detection efficiency, consistency, and diagnostic accuracy, an automated microscopic image
scanning system was developed and tested to directly acquire digital images with sufficient spatial resolution for clinical
diagnosis. A computer-aided detection (CAD) scheme was also developed and integrated into the image scanning system
to search for and detect the regions of interest (ROI) that contain analyzable metaphase chromosome cells in the large
volume of scanned images acquired from one specimen. Thus, the cytogeneticists only need to observe and interpret the
limited number of ROIs. In this study, the high-resolution microscopic image scanning and CAD performance was
investigated and evaluated using nine sets of images scanned from either bone marrow (three) or blood (six) specimens
for diagnosis of leukemia. The automated CAD-selection results were compared with the visual selection. In the
experiment, the cytogeneticists first visually searched for the analyzable metaphase chromosome cells from specimens
under microscopes. The specimens were also automated scanned and followed by applying the CAD scheme to detect
and save ROIs containing analyzable cells while deleting the others. The automated selected ROIs were then examined
by a panel of three cytogeneticists. From the scanned images, CAD selected more analyzable cells than initially visual
examinations of the cytogeneticists in both blood and bone marrow specimens. In general, CAD had higher performance
in analyzing blood specimens. Even in three bone marrow specimens, CAD selected 50, 22, 9 ROIs, respectively. Except
matching with the initially visual selection of 9, 7, and 5 analyzable cells in these three specimens, the cytogeneticists
also selected 41, 15 and 4 new analyzable cells, which were missed in initially visual searching. This experiment showed
the feasibility of applying this CAD-guided high-resolution microscopic image scanning system to prescreen and select
ROIs that may contain analyzable metaphase chromosome cells. The success and the further improvement of this
automated scanning system may have great impact on the future clinical practice in genetic laboratories to detect and
diagnose diseases.
Fluorescence in situ hybridization (FISH) technology has been widely recognized as a promising molecular and biomedical optical imaging tool to screen and diagnose cervical cancer. However, manual FISH analysis is time-consuming and may introduce large inter-reader variability. In this study, a computerized scheme is developed and tested. It automatically detects and analyzes FISH spots depicted on microscopic fluorescence images. The scheme includes two stages: (1) a feature-based classification rule to detect useful interphase cells, and (2) a knowledge-based expert classifier to identify splitting FISH spots and improve the accuracy of counting independent FISH spots. The scheme then classifies detected analyzable cells as normal or abnormal. In this study, 150 FISH images were acquired from Pap-smear specimens and examined by both an experienced cytogeneticist and the scheme. The results showed that (1) the agreement between the cytogeneticist and the scheme was 96.9% in classifying between analyzable and unanalyzable cells (Kappa=0.917), and (2) agreements in detecting normal and abnormal cells based on FISH spots were 90.5% and 95.8% with Kappa=0.867. This study demonstrated the feasibility of automated FISH analysis, which may potentially improve detection efficiency and produce more accurate and consistent results than manual FISH analysis.
Interphase fluorescence in situ hybridization (FISH) technology is a potential and promising molecular imaging
tool, which can be applied to screen and detect cervical cancer. However, manual FISH detection method is a subjective,
tedious, and time-consuming process that results in a large inter-reader variability and possible detection error (in
particular for heterogeneous cases). Automatic FISH image analysis aims to potentially improve detection efficiency and
also produce more accurate and consistent results. In this preliminary study, a new computerized scheme is developed to
automatically segment analyzable interaphase cells and detect FISH signals using digital fluorescence microscopic
images acquired from Pap-smear specimens. First, due to the large intensity variations of the acquired interphase cells
and overlapping cells, an iterative (multiple) threshold method and a feature-based classifier are applied to detect and
segment all potentially analyzable interphase nuclei depicted on a single image frame. Second, a region labeling
algorithm followed up a knowledge-based classifier is implemented to identify splitting and diffused FISH signals.
Finally, each detected analyzable cell is classified as normal or abnormal based on the automatically counted number of
FISH signals. To test the performance of this scheme, an image dataset involving 250 Pap-smear FISH image frames
was collected and used in this study. The overall accuracy rate for segmenting analyzable interphase nuclei is 86.6%
(360/424). The sensitivity and specificity for classifying abnormal and normal cells are 88.5% and 86.6%, respectively.
The overall cell classification agreement rate between our scheme and a cytogeneticist is 86.6%. The testing results
demonstrate the feasibility of applying this automated scheme in FISH image analysis.
An integrated computer-aided detection (CAD) scheme was developed for detecting and classifying metaphase chromosomes. The CAD scheme's performance and robustness is assessed. This scheme includes an automatic metaphase-finding module and a karyotyping module, and it was applied to a testing database with 200 digital microscopic images. The automatic metaphase-finding module detects analyzable metaphase cells using a feature-based artificial neural network (ANN). The ANN-generated outputs are analyzed by a receiver operating characteristics (ROC) method, and the area under the ROC curve is 0.966. Then, the automatic karyotyping module classifies individual chromosomes of this cell into 24 types. In this module, a two-layer decision tree-based classifier with eight ANNs established in its connection nodes was optimized by a genetic algorithm. Chromosomes are first classified into seven groups by the ANN in the first layer. The chromosomes in these groups are then separately classified by seven ANNs into 24 types in the second layer. The classification accuracy is 94.5% in the first layer. Six ANNs achieved the accuracy above 95% and only one had lessened performance (80.6%) in the second layer. The overall classification accuracy is 91.5% as compared with 86.7% in the previous study using two independent datasets randomly acquired from our genetic laboratory. The results demonstrate that this automated scheme achieves high and robust performance in identification and classification of metaphase chromosomes.
Scanning of microscope slides is an important part of cytogenetic diagnosis. Metaphase chromosomes arranged
in a karyotype reveal the nature and severity of cancer and other diseases. Searching for metaphases spreads is a lengthy
and tedious process that can benefit from computer aided systems. When slides are searched by such systems in
continuous motion, the image quality is reduced. The motion blur is a function of the scan speed, the camera frame rate
and sample time, and the level of magnification. In this study, normalized contrast transfer function (CTF) is used to
define the amount of image degradation.
Our integrated computer-aided detection (CAD) scheme includes three basic modules. The first module detects
whether a microscopic digital image depicts a metaphase chromosome cell. If a cell is detected, the scheme will justify
whether it is analyzable with a decision tree. Once an analyzable cell is detected, the second module is applied to
segment individual chromosomes and to compute two important features. Specifically, the scheme utilizes a modified
thinning algorithm to identify the medial axis of a chromosome. By tracking perpendicular lines along the medial axis,
the scheme computes four feature profiles, identifies centromeres, and assigns polarities of chromosomes based on a set
of pre-optimized rules. The third module is followed to classify chromosomes into 24 types. In this module, each
chromosome is initially represented by a vector of 31 features. A two-layer classifier with 8 artificial neural networks
(ANN) is optimized by a genetic algorithm. A testing chromosome is first classified into one of the seven groups by the
ANN in the first layer. Another ANN is then automatically selected from the seven ANNs in the second layer (one for
each group) to further classify this chromosome into one of 24 types. To test the performance and robustness of this
CAD scheme, we randomly selected and assembled an independent testing dataset. The dataset contains 100 microscopic
digital images including 50 analyzable and 50 un-analyzable metphase cells identified by the experts. The centromere
location, the corresponding polarity, and karyotype for each individual chromosome were recorded in the "truth" file.
The performance of the CAD scheme applied to this image dataset is analyzed and compared with the results in the true
file. The assessment accuracies are 93% for the first module, 90.8% for centromere identification and 93.2% for polarity
assignment in the second module, over 96% for six chromosome groups and 81.8% for one group in the third module,
respectively. These accuracy levels are very comparable with those achieved during our previous studies to develop and
optimize these CAD modules. Hence, the study demonstrates that our automated scheme can achieve high and robust
performance in identification and classification of metaphase chromosomes.
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