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BioImage Suite is an integrated image analysis software suite
developed at Yale. It uses a combination of C++ and Tcl in the same
fashion as that pioneered by the Visualization Toolkit (VTK) and it
leverages both VTK and the Insight Toolkit. It has [...]
Cerebral Cortical Thickness Estimation using the TINA
Open-Source Image Analysis Environment
Published in The Insight Journal
Published in The Insight Journal
This paper gives an overview of the use and development of the TINA open-source medical image analysis environment, with respect to the determination of human cerebral cortical thickness estimation from magnetic resonance images. The ultimate aim of TINA is [...]
BioImage Suite: An integrated medical image analysis suite: An update
Published in The Insight Journal
Published in The Insight Journal
BioImage Suite is an NIH-supported medical image analysis software suite developed at Yale. It
leverages both the Visualization Toolkit (VTK) and the Insight Toolkit (ITK) and it includes many additional
algorithms for image analysis especially in the areas [...]
We have successfully created a software environment in which ultrasound data can be manipulated by, ITK (the Insight Tool-Kit), in real-time. We were able to access each frame generated within the resident computer of a TerasonTM Ultrasound Machine, convert [...]
Visualizing metabolic phenotypes, tracking phenotype dynamics, and screening molecular interventions all require comprehensive,
quantitative measures of micromolecular patterns across cell classes. In this project we develop an easy-to-use interface that [...]
To facilitate the analysis of medical image data in research environment, MATITK is developed to allow ITK algorithms to be called in MATLAB. ITK is a powerful open-source image analysis toolkit, but it requires the knowledge of C++ to use it. With the help [...]
Combining some labeled images is a quite common and useful task in image analysis.
That's something we may want to do to prepare the markers for a watershed from
markers for example, or to write the output of several segmentations in a single
file.
This [...]
Biomarker Detection in Whole Slide Imaging based on Statistical Color Models
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper presents a technique for immunostaining biomarker detection in digital slides. We treat immunostaining detection as a color image analysis problem and build statistical color models using a large number of labeled positive and negative [...]
Convolution is a basic operation in image analysis and the Insight Toolkit provides a well-framed mechanism for such operations (see Chapter 11 of the ITK Software Guide. The classes associated with this contribution are meant to simplify convolution [...]
This document presents a set of classes (vtkPhysicalCamera, vtkImageCamera) to enable a camera and an image acquired by that camera to be visualized in a 3D scene. Two situations where one would want to visualize camaras with associated images are range data [...]
We have previously developed an algorithm for locating boundaries in an image with sub-pixel resolution, as well as estimating boundary width and image intensity within the adjoining objects. The algorithm operates by finding the parameters of a cumulative [...]
A novel atlas-selection approach for multi-atlas based segmentation using the correlation of inter-atlas similarities
Published in The MIDAS Journal
Published in The MIDAS Journal
Automated segmentation is a frequently applied task in the course of medical imaging. Furthermore, it is a substantial component of image-guided radiotherapy. Atlas based segmentation is one of the most frequently used approach for automated segmentation. [...]
Transitively Consistent and Unbiased Multi-Image Registration using Numerically Stable Transformation Synchronisation
Published in The MIDAS Journal
Published in The MIDAS Journal
Transitive consistency of pairwise transformations is a desirable property of groupwise image registration procedures. The transformation synchronisation method (Bernard et al., 2015) is able to retrieve transitively consistent pairwise transformations from [...]
Unified framework for development, deployment and testing of image analysis algorithms
Published in The MIDAS Journal
Published in The MIDAS Journal
Developing both graphical and command-line user interfaces for image analysis algorithms requires considerable effort. Generally developers provide limited to very rudimentary user interface controls to their users. These image analysis algorithms can only [...]
The gestational age (GA) determination is one of the most used measures to guide diagnostics of specialists in neonatology to
guarantee the newborn surveillance. However, the currently available methods have been subject to a number of evaluations and [...]
Adaptations of MARACAS algorithm to the segmentation of the carotid bifurcation and stenosis quantification in CTA images
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper describes a 3D CTA image segmentation method submitted to the CLS09 contest (Carotid Lumen Segmentation and Stenosis Quantification) held in conjunction with the MICCAI 2009 conference. First, images are denoised to improve image quality and [...]
Coronary centerline tracking in CT images with use of an elastic model and image moments.
Published in The MIDAS Journal
Published in The MIDAS Journal
This coronary-artery extraction method uses one initialization point per vessel. First, a mask is computed by use of a region-growing algorithm, which starts from the initial point and stops when no more connected voxels fall within an interactively defined [...]
Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation
Published in The Insight Journal
Published in The Insight Journal
Modern medical imaging analyses often involve the concatenation of multiple steps, and neuroimaging analysis is no exception. The Java Image Science Toolkit (JIST) has provided a framework for both end users and engineers to synthesize processing modules into [...]
Medical image analysis is an important problem relating to
the study of various diseases. Since their inception to MICCAI in
2001, ''deformable organisms'' have emerged as a fruitful
methodology with examples ranging from 2D corpus callosum
segmentation [...]
Although Gabor filtering is quite prevalent in the computer vision community for such tasks as
texture segmentation and motion analysis, such capabilities are conspicuously absent from the
Insight Toolkit. The contribution described in this paper attempts [...]
For over two decades, the National Library of Medicine (NLM)
has provided support for the collection of biomedical image data for use
throughout the biomedical image, visualization and analysis community.
Data collected during the Visible Human Project has [...]
This document describes a new remote module implemented for the Insight Toolkit (ITK), itkBoneMorphometry. This module contains bone analysis filters that compute features from N-dimensional images that represent the internal architecture of bone. The [...]
Being able to quickly compute the inverse of a deformation field is often useful in the context of medical image analysis. While ITK supports this functionality, the current algorithms are slow and do not always yield accurate results. In this paper we [...]
In previous work, we presented an algorithm to synthesize volumetric images of vascular trees and generate the corresponding ground truth segmentations, bifurcation locations, branch properties, and tree hierarchy. In this work, we provide the software needed [...]
In this document it is described the implementation of the flux driven automatic centerline extraction
algorithm proposed by Bouix et al. in 2004. This is based on a skeletonisation algorithm initially
proposed by Siddiqi et al. in 2002, using properties of [...]
Non-destructive evaluation(NDE) is a group of analysis techniques used in industry to evaluate the property of a material, component or product without causing damage. Among all the techniques, radiology and thermography are two most common methods that are [...]
Nonrigid image registration is an important, but resource demanding and time-consuming task in medical image analysis. This limits its application in time-critical clinical routines. In this report we explore acceleration of two time-consuming parts of a [...]
An Intelligent cluster-based segmentation using Wavelet Features:Application to Medical Images
Published in The MIDAS Journal
Published in The MIDAS Journal
Segmentation forms the onset for image analysis especially for medical images, making any abnormalities in tissues distinctly visible. Possible application includes the detection of tumor boundary in SPECT, MRI or electron MRI (EMRI). Nevertheless, tumors [...]
The Lung Tissue Research Consortium: An extensive open database containing histological, clinical, and radiological data to study chronic lung disease
Published in The Insight Journal
Published in The Insight Journal
The Lung Tissue Research Consortium (LTRC) is an NHLBI sponsored project which is studying histological, radiological, and clinical data on patients with Chronic Obstructive Pulmonary Disease (COPD) and idiopathic pulmonary fibrosis (IPF). At completion, [...]
FusionViewer: An Open Source Toolkit for Viewing Multimodality Images
Published in The Insight Journal
Published in The Insight Journal
FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) [...]
We have created open-source Simulink block libraries for ITK and VTK that allow pipelines for these toolkits to be built in a visual, drag-and-drop style within MATLAB. Each block contains an instance of an ITK or VTK class. Any block connections and [...]
A programming environment for the development of modular 3D biomedical image processing applications
Published in The Insight Journal
Published in The Insight Journal
ImageLib is a free object-oriented development environment destined to biomedical image processing. The software package contains a programming library (C++ language) and an MDI user interface (kernel). The major interest is to allow the creation of fully [...]
The itkLabelGeometryImageFilter is a new ITK filter that enables the measurement of geometric features of labeled objects. It calculates features similar to the "regionprops" command of Matlab. It is related to the itkLabelStatisticsImageFilter in that both [...]
