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Tiff images are widely used and domain and instrument specific
information is often included in some tags. There isn't any standard
way of making use of this information in ITK at present. This article
introduces some minor additions to the ITK tiff reader to [...]
In this submission, we offer the GaussianInterpolationImageFunction which adds to the growing collection of existing interpolation algorithms in ITK for resampling scalar images such as the LinearInterpolateImageFunction, BSplineInterpolateImageFunction, and [...]
This paper describes how to compile and use the Insight Toolkit Kinetic Analysis library (itk::ka), to perform analysis of dynamic medical images, along with a brief overview of the library source code. Supplied, are a set of interfaces to facilitate [...]
This document describes the implementation of image samplers using the Insight Toolkit ITK url{www.itk.org}. Image samplers take a set of `picks' from an image and store them in an array. A sample consists of the location of the pick (a point) and the [...]
We have modified the current VTK volume rendering on GPU to allow simultaneous rendering of two volumes, each of them with its own color and opacity transfer functions.
These changes have led to the creation of two new C++ classes and several GLSL shaders. We [...]
We present a filter that voxelizes the volume of a 3D structured, unstructured, or rectilinear grid into a vtkImageData with partial volume effects. The partial grid volume occupying each voxel is computed exactly from the intersection of the grid volume and [...]
This paper describes a set of pixel accessors that transform RGB pixel values to a different color space. Accessors for the HSI, XYZ, Yuv, YUV, HSV, Lab, Luv, HSL, CMY, and CMYK color spaces are provided here. This paper is accompanied with source code for [...]
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
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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 [...]
Two Point Minimum Cost Path Approach for CTA Coronary Centerline Extraction
Published in The MIDAS Journal
Published in The MIDAS Journal
In this work a minimum cost path approach is adopted to extract coronary artery centerlines from CTA data. The algorithm depends on the manual definition of the start and end point of the vessel. The cost image used in the minimal cost path approach is based [...]
Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning
Published in The MIDAS Journal
Published in The MIDAS Journal
In radiation treatment (RT) planning medical doctors need to consider a variety of information sources for anatomical and functional target volume delineation. The validation and inspection of the defined target volumes and the resulting RT plan is a complex [...]
Adding Refined Isosurface Rendering and Shadow Mapping to vtkGPUVolumeRayCastMapper
Published in The VTK Journal
Published in The VTK Journal
In the medical simulation world the use of isosurfaces is a common action, as the information from some sources, e.g. CTs, is very well defined, and the isosurface can be easily set. Additionally, in any simulator shadows are a necessary addition to increase [...]
This code provides an implementation of a simple technique to fill small holes in an image. We use a multi-pass method that fills pixels on the border of a hole with the average of its non-hole 8-connected neighbors. This process is repeated until all holes [...]
This document presents a GUI application to manually select corresponding points in two data sets. The data sets can each be either an image or a point cloud. If both data sets are images, the functionality is equivalent to Matlab's 'cpselect' function. There [...]
Recently, an implementation of the Vessel Enhancing Diffusion (VED) algorithm [3] using the Insight Toolkit (ITK) framework [2] has been proposed by Enquobahrie et al.[1]. In this paper we present an alternative implementation, for two reasons. First, in this [...]
Isotropic and Steerable Wavelets in N Dimensions. A multiresolution analysis framework.
Published in The Insight Journal
Published in The Insight Journal
This document describes the implementation of the external module ITKIsotropicWavelets, a multiresolution (MRA) analysis framework using isotropic and steerable wavelets in the frequency domain. This framework provides the backbone for state of the art [...]
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 [...]
Junctions of tubular structures (vasculature, trachea, neuron, etc) in medical images are critical for the topology of these structures. Identification of them is helpful in many applications. For example, quantification of geometric vascular features, [...]
Enabling ITK-based processing and 3D Slicer MRML scene management in ParaView
Published in The VTK Journal
Published in The VTK Journal
This paper documents on-going work to facilitate ITK-based processing and 3D Slicer scene management in ParaView. We believe this will broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The [...]
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 [...]
A new implementation of itk::ImageToImageFilter for efficient parallelization of image processing algorithms using Intel Threading Building Blocks
Published in The Insight Journal
Published in The Insight Journal
Modern medical imaging makes use of high performance computing to accelerate image acquisition, image reconstruction, image visualization and image analysis. Software libraries that provide implementations of key medical imaging algorithms need to efficiently [...]
This paper presents parsing software for importing contours from DICOM RT structure set files into binary image files. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image [...]
This document describes a plug-in for Blender (www.blender.org) that allows to rasterize 3D mesh objects into 3D voxel data, i. e. it allows to voxelize Blender meshes. In 2D, this process can be compared to rasterization of vector graphics into pixel [...]
This paper presents code for reading contours from DICOM RT structure set files into binary labels. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image analysis [...]
On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands
Published in The MIDAS Journal
Published in The MIDAS Journal
The segmentation of parotid glands in CT scans of patients with head and neck cancer is an essential part of treatment planning. We introduce a new method for the automatic segmentation of parotid glands that extends existing patch-based approaches in three [...]
This document describes a new class that takes an doxygen{Transform} and
evaluates the deformation at points in a user-defined region.
The class is implemented using the Insight Toolkit url{www.itk.org}.
This paper is accompanied with the source code, [...]
Multimodal Analysis of Vasogenic Edema in Glioblastoma Patients for Radiotherapy Planning
Published in The MIDAS Journal
Published in The MIDAS Journal
Glioblastoma (GBM) is the most common type of primary
brain tumor, which is characterized by an infiltrative growth pattern.
In current practice, radiotherapy planning is primarily based upon T2
FLAIR MRI despite its known lack of specificity in the detection [...]
We have implemented filters for computing phase symmetry (PS) in ITK using steerable filters computed and applied in the Fourier domain. In some recent publications, phase symmetry has been shown to be a useful pre-processing measure for performing image [...]
This document describes an implementation of David S. Tuch's numerical Q-Ball reconstruction algorithm implemented using the Insight Toolkit ITK (www.itk.org). The document is accompanied with the source code, input data, parameters and output data that were [...]
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy
Published in The Insight Journal
Published in The Insight Journal
This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion's demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver [...]
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 [...]
ly in ITK, the only way to find the contour of the objects in a binary image is to use the BinaryErodeImageFilter, with a kernel of radius 1. This filter is a generic filter, made to support any shape and size of structuring element, and thus is not optimized [...]
This paper describes the Statismo framework, which is a framework for PCA based statistical models.Statistical models are used to describe the variability of an object within a population, learned from a set of training samples. Originally developed to model [...]
In this article, a spline driven image slicer algorithm is presented. It is concretized through a vtkAlgorithm-inherited class that takes two inputs and gives two outputs. The first input is the volume from which the slice should reconstructed while the [...]
The contribution to VTK presented in this article is an extension to vtk::vtkDiscreteMarchingCubes to also create vtk::vtkPointData scalars containing the value of the adjacent voxel. These can be used to remove regions of the marching-cubes 1 mesh depending [...]
Efficient multithreading for manycore processor: Multidimensional domain decomposition using Intel® TBB
Published in The Insight Journal
Published in The Insight Journal
The Insight Toolkit (ITK) utilizes a generic design for image processing filters that allows many developers to rapidly implement new algorithms. While ITK filters benefit from a platform-independent and versatile multithreading capability, the current [...]
We have recently detailed the procedure for building ITK on the iOS. In this work, we contribute itkiOSImageIO , the necessary ITK class that provides the input/output (IO) interface with the repository of images stored on iOS Apple devices, such as the iPod [...]
This program, based completely on ITK, converts between the different file types available in the ITK. Casting between the different pixel component types is available as an option. Currently, only scalar pixel types are supported.
This document describes a new remote module implemented for the Insight Toolkit ITK, itkTextureFeatures. This module contains two texture analysis filters that are used to compute feature maps of N-Dimensional images using two well-known texture analysis [...]
In this work,
we extend a previously demonstrated entropy based groupwise registration method
to include a non-rigid deformation model based on B-splines.
We describe an open source implementation of the groupwise registration algorithm
using the [...]
Facet Analyser: ParaView plugin for automated facet detection and measurement of interplanar angles of tomographic objects
Published in The MIDAS Journal
Published in The MIDAS Journal
The presented ParaView plugin allows easy access to the algorithm described in Ref 1. It enables analysis of faceted objects that exhibit distortions in their digital representation, e.g. due to tomographic reconstruction artifacts.
The contributed [...]
Richard Beare has recently introduced a new filter to efficiently labelize the connected components with ITK, and has also proposed to use the run-length encoding used in that filter to implement some of the most useful binary mathematical morphology [...]
An ITK Implementation of the Symmetric Log-Domain Diffeomorphic Demons Algorithm
Published in The Insight Journal
Published in The Insight Journal
This article provides an implementation of the symmetric log-domain diffeomorphic image registration algorithm, or symmetric demons algorithm for short. It generalizes Thirion's demons and the diffeomorphic demons algorithm. The main practical advantages of [...]
At the Johns Hopkins University’s Engineering Research Center for Computer-Integrated Surgical Systems and Technology (ERC-CISST) laboratory, we have designed and developed a platformindependent C++ software package, called the nArray library, that provides [...]
An entropy based multi-thresholding method for semi-automatic segmentation of liver tumors
Published in The MIDAS Journal
Published in The MIDAS Journal
Liver cancer is the fifth most commonly diagnosed cancer and the third most common cause of death
from cancer worldwide. A precise analysis of the lesions would help in the staging of the tumor and
in the evaluation of the possible applicable therapies. In [...]
