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We describe a new collection of publicly available software tools for performing quantitative neuroimage analysis. The tools perform semi-automatic brain extraction, tissue classification, Talairach alignment, and atlas-based measurements within a user-friendly graphical environment. They are implemented as plug-ins for MIPAV, a freely available medical(More)
We describe the construction and use of a compact dual-view inverted selective plane illumination microscope (diSPIM) for time-lapse volumetric (4D) imaging of living samples at subcellular resolution. Our protocol enables a biologist with some prior microscopy experience to assemble a diSPIM from commercially available parts, to align optics and test(More)
OBJECTIVE The aim of this study was to evaluate a 3D tumor segmentation method for fluorodeoxyglucose positron emission tomography (FDG-PET) in the context of noninvasive estimation of tumor metabolic length (Lm), as it correlates with surgical pathology and phantom results. METHODS Thirty-four patients (7 women, 27 men) with esophageal cancer were(More)
Logarithmic amplifiers (log amps), which produce an output signal proportional to the logarithm of the input signal, are widely used in cytometry for measurements of parameters that vary over a wide dynamic range, e.g., cell surface immunofluorescence. Existing log amp circuits all deviate to some extent from ideal performance with respect to dynamic range(More)
Automatic prostate segmentation in MR images is a challenging task due to inter-patient prostate shape and texture variability, and the lack of a clear prostate boundary. We propose a supervised learning framework that combines the atlas based AAM and SVM model to achieve a relatively high segmentation result of the prostate boundary. The performance of the(More)
This work presents a MRI prostate segmentation and surface reconstruction model that facilities the validation of multi-parametric MRI with histopathology slides from radical prostatectomy specimens and targeted biopsy specimens. Application of this technique combines image processing and computer aided design to provide a generalized solution to construct(More)