Insight Journal

The Insight Journal is an Open Access on-line publication covering the domain of medical image processing and visualization.

The unique characteristics of the Insight Journal include:

- Open-access to articles, data, code, and reviews
- Open peer-review that invites discussion between reviewers and authors
- Emphasis on reproducible science via automated code compilation and testing
- Support for continuous revision of articles, code, and reviews

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A Flexible Variational Registration Framework
Published in The Insight Journal

Schmidt-Richberg A., Werner R., Handels H., Ehrhardt J.

In this article, we present an implementation of a flexible framework for non-parametric variational image registration, realized as part of ITK's finite difference solver hierarchy. In a variational registration setting, the transformation is found by [...]

downloaded 4341 times, viewed 1096 times and no review.

A MultipleImageIterator for iterating over multiple images simultaneously
Published in The Insight Journal

Schaerer J.

Several applications such as multi-atlas segmentation require frequent iteration over multiple image volumes at the same time. Doing so with the regular ITK iterators is tedious and error prone as it requires updating each iterator at end of each iteration. [...]

downloaded 3851 times, viewed 967 times and no review.

Using TubeTK to Automatically Merge Volumes
Published in The Insight Journal

Mullins C., Gessner R., Aylward S.

This article describes implementation of a CLI module to merge an image into the space of another adjacent image using the Insight Toolkit. The algorithm constructs a smoothly stitched image out of two or more smaller images. The overlapping regions of the [...]

downloaded 2922 times, viewed 838 times and no review.

STL file format MeshIO class for ITK
Published in The Insight Journal

Ibanez L.

This document describes the implementation of an ITK class to support the reading and writing of Meshes in STL file format. The Meshes are assumed to contain 2D manifolds embedded in a 3D space. In practice, it would be desirable to use this class mostly to [...]

downloaded 3976 times, viewed 1018 times and no review.

BinShrink: A multi-resolution filter with cache efficient averaging.
Published in The Insight Journal

Lowekamp B., Chen D.

We present a new filter for the Insight Toolkit (ITK) for reducing the resolution of an image by an integer factor while averaging called BinShrink. This filter provides a new level of performance to ITK for reducing resolution and noise present in an image. [...]

downloaded 3324 times, viewed 831 times and no review.

The Image-based Vascular Analysis Toolkit (IvanTk)
Published in The Insight Journal

Macia I.

This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an [...]

downloaded 4103 times, viewed 809 times and no review.

GPU and CPU implementation of Young - Van Vliet's Recursive Gaussian Smoothing Filter

GPU and CPU implementation of Young - Van Vliet's Recursive Gaussian Smoothing Filter
Published in The Insight Journal

Vidal-Migallon I., Commowick O., Pennec X., Dauguet J., Vercauteren T.

This document describes an implementation for GPU and CPU of Young and Van Vliet's recursive Gaussian smoothing as an external module for the Insight Toolkit ITK, version 4.* www.itk.org. In the absence of an OpenCL-capable platform, the code will run the CPU [...]

downloaded 4534 times, viewed 946 times and 3 reviews.

Laplacian Mesh Deformation
Published in The Insight Journal

Gelas A.

Deforming a 3D surface mesh while preserving its local detail is useful for editing anatomical atlases or for mesh based segmentation. This contribution introduces new classes for performing hard and soft constraints deformation in a flexible design which [...]

downloaded 14745 times, viewed 913 times and 1 reviews.

Importing Contours from DICOM-RT Structure Sets with ITK4

Importing Contours from DICOM-RT Structure Sets with ITK4
Published in The Insight Journal

Dowling J.

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 [...]

downloaded 5818 times, viewed 1428 times and 2 reviews.

Parallel algorithms for erosion and dilation of label images.

Parallel algorithms for erosion and dilation of label images.
Published in The Insight Journal

Beare R., Jackway P.

It is sometimes useful to be able to apply binary morphological operations, such as erosions and dilations, to labelled images in a fashion that preserves the labels. This article introduces a specialised class implementing parallel methods described in beare [...]

downloaded 5060 times, viewed 949 times and 2 reviews.

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