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A programming environment for the development of modular 3D biomedical image processing applications
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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 [...]

Applying Image Mining to Support Gestational Age Determination
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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 [...]

A Fast Approximation to the Bilateral Filter for ITK
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This document describes an implementation of an alternative bilateral filtering algorithm in ITK. This class implements the fast bilateral filter algorithm in ITK by taking the input image and organizing it into the required data structure as an ITK Image [...]

MITK and 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems
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This paper introduces an integrated 3D medical image processing and analyzing software platform which is open interface and freely available. The platform consists of the Medical Imaging Toolkit (MITK) and the 3-Dimensional Medical Image Processing [...]

Guided Diffusion Tensor Tractography with GTRACT: A Validation Study
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A novel fiber tracking algorithm (GTRACT) was developed to enhance tracking through ambiguous regions where cross fibers, fiber merging or fanning may be occurring. The software was developed using several cross platform open-source toolkits (ITK, VTK, and [...]

Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation
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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 [...]

An OpenCL implementation of the Gaussian pyramid and the resampler
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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 [...]

Direct Fourier Tomographic Reconstruction Image-To-Image Filter
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We present an open-source ITK implementation of a direct Fourier method for tomographic reconstruction, applicable to parallel-beam x-ray images. Direct Fourier reconstruction makes use of the central-slice theorem to build a polar 2D Fourier space from the [...]

Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK
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The Allen Brain Atlas (ABA) project aims to create a cellular-resolution, genome-wide map of gene expression in the adult mouse brain. The resulting in situ hybridization (ISH) image data will be available free-of-charge to the public. Additionally, we [...]

Alternative Memory Models for ITK Images
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By default ITK images use a contiguous memory model. This means pixel elements are stored in a single 1-D array, where each element is adjacent in memory to the previous element. However in some situations it is not desirable to use this memory model. This [...]

RLEImage: run-length encoded memory compression scheme for an itk::Image
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This document describes a new class, itk::RLEImage, which uses run-length encoding to reduce the memory needed for storage of label maps. This class is accompanied by all the iterators to make it a dropin replacement for itk::Image. By changing the image [...]

ND morphological contour interpolation
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This document describes a new class, itk::MorphologicalContourInterpolator, which implements a method proposed by Albu et al. in 2008. Interpolation is done by first determining correspondence between shapes on adjacent segmented slices by detecting overlaps, [...]

Real-Time Ultrasound Image Analysis for the Insight Toolkit
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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 [...]

MUSiiC ToolKit 2.0: Bidirectional Real-time Software Framework for Advanced Interventional Ultrasound Research
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Ultrasound (US) imaging is a popular and convenient medical imaging modality thanks to its mobility, non-ionizing radiation, ease-of-use, and real-time acquisition. Conventional US imaging is frequently integrated with tracking systems and robotic systems in [...]

Support for
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VoxBo (www.voxbo.org) is a distributed processing framework, developed at the Center of Functional Neuroimaging at the University of Penssylvania, with the purpose of processing and analyzing brain functional MRI data. VoxBo is written in C++, and it is [...]

The Generalised Image Fusion Toolkit (GIFT)
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Image fusion provides a mechanism to combine multiple images into a single representation to aid human visual perception and image processing tasks. Such algorithms endeavour to create a fused image containing the salient information from each source image, [...]

The NLM-Mayo Image Collection: Common Access to Uncommon Data
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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 [...]

Cerebral Cortical Thickness Estimation using the TINA
  Open-Source Image Analysis Environment
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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
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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 [...]

Open Source Software in the Development and Testing of an Image-Guided Robot System
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This paper describes the use of open source software in the development and testing of an image-guided robot system for small animal research, presented at MICCAI 2006. This system relied on a significant amount of open source software, including 3D [...]

An open, clinically-validated database of 3D+t cine-MR images of the left ventricle with associated manual and automated segmentation
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In this paper, we describe a database of cine-MR (3D+t) images of the left ventricle. This database contains the voxel data, one automated and two manual segmentations for each sequence of images. The segmentations are validated from a clinical point of [...]

Segmentation of the Left Ventricle from Cine MR Images Using a Comprehensive Approach
No opinion
Segmentation of the left ventricle is important in assessment of cardiac functional parameters. Currently, manual segmentation is the gold standard for acquiring these parameters and can be time-consuming. Therefore, accuracy and automation are two important [...]

MATITK: EXTENDING MATLAB WITH ITK
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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 [...]

BioImage Suite: An integrated medical image analysis suite: An update
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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 [...]

An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open-source software
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This paper describes a new open-source tutorial for image-guided therapy (IGT) and medical robotics that is both accessible and hands-on using the LEGO Mindstorms NXT (a commercially available robotics kit) and 3D Slicer (an open-source application for [...]

Simulink Libraries for Visual Programming of VTK and ITK
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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 [...]

The Lung Tissue Research Consortium:  An extensive open database containing histological, clinical, and radiological data to study chronic lung disease
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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, [...]

Tetrahedral mesh generation for medical imaging
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We describe the open source implementation of an adaptive tetrahedral mesh generator particularly targeted for non-rigid FEM registration of MR images. While many medical imaging applications require robust mesh generation, there are few codes available. [...]

A Label Geometry Image Filter for Multiple Object Measurement
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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 [...]


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