Image Processing

The mechanical properties of cells and tissues play a well-known role in physiology and disease. The model organism Caenorhabditis elegans exhibits mechanical properties that are still poorly understood, but are thought to be dominated by its collagen-rich outer cuticle. To our knowledge, we use a novel microfluidic technique to reveal that the worm responds linearly to low applied hydrostatic stress, exhibiting a volumetric compression with a bulk modulus, k ¼ 140 5 20 kPa; applying negative pressures leads to volumetric expansion of the worm, with a similar bulk modulus. Surprisingly, however, we find that a variety of collagen mutants and pharmacological perturbations targeting the cuticle do not impact the bulk modulus. Moreover, the worm exhibits dramatic stiffening at higher stresses-behavior that is also independent of the cuticle. The stress-strain curves for all conditions can be scaled onto a master equation, suggesting that C. elegans exhibits a universal elastic response dominated by the mechanics of pressurized internal organs.

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“…Time-lapse sequences of images were processed using IMAGEJ (National Institutes of Health, Bethesda, MD) (35) and MATLAB (The MathWorks,…”

Section: Image Analysismentioning

confidence: 99%

Worms under Pressure: Bulk Mechanical Properties of C. elegans Are Independent of the Cuticle

Gilpin

Uppaluri

Brangwynne

2015

Biophysical Journal

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“…Regions of interest were placed using ImageJ (Abramoff et al, 2004) on the corpus callosum from the RGB map as described by Lodygensky et al (2010).…”

Section: Post-processingmentioning

confidence: 99%

In vivo assessment of myelination by phase imaging at high magnetic field

et al. 2012

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The present study evaluated the potential of using the phase of T 2 * weighted MR images to characterize myelination during brain development and pathology in rodents at 9.4 T. Phase contrast correlated with myelin content assessed by histology and suggests that most contrast between white and cortical gray matter is modulated by myelin. Ex vivo experiments showed that gray-white matter phase contrast remains unchanged after iron extraction. In dysmyelinated shiverer mice, phase imaging correlated strongly with myelin staining, showing reduced contrast between white and gray matter when compared to healthy controls. We conclude that highresolution phase images, acquired at high field, allow assessment of myelination and dysmyelination.© 2011 Elsevier Inc. All rights reserved. IntroductionThe assessment of myelination in healthy subjects and following injury in humans and in animal models is one of the ways to determine the degree of cerebral integrity or the degree of injury in case of white matter disease like multiple sclerosis. In newborns, myelination of the posterior limb of the internal capsule, when assessed at term equivalent, has been shown to be a very robust predictor of motor impairment (Cowan and de Vries, 2005). A simple technique that would access the degree of myelination of white matter would be very useful in mature animal models of white matter injury such as multiple sclerosis and in immature animal models of white matter injury such as periventricular leukomalacia as well as in human studies. There are various methods available: one approach consists of quantification of myelin bond and free water fractions by a multiexponential analysis of the T 2 decay (Beaulieu et al., 1998;MacKay et al., 1994;Whittall and MacKay, 1989;Lancaster et al., 2003). This is generally performed using a CarrPurcell-Meiboom-Gill (CPMG) or a Turbo Spin-Echo sequences with multiple echo times (Beaulieu et al., 1998). Due to specific absorption rate (SAR) (especially at high fields) and timing constraints, the T 2 decay curve is often not fully sampled for an accurate quantification. Recently, it has been shown that myelin water fraction can also be measured using a multi-exponential analysis of the T 2 * decay in multislice multiple echo gradient echo sequence (Du et al., 2007;Hwang et al., 2010). The resulting myelin water fractions are highly dependent on the constraints introduced on the multi-exponential fitting procedure (Hwang et al., 2010) and suffer from significant inaccuracies in regions close to air-tissue interfaces. An alternative approach of a multicomponent relaxation analysis using multicomponent driven equilibrium single pulse observation of T1 and T2 (mcDESPOT) (Deoni et al., 2008) was applied successfully on infants from 3 to 11 months to quantify myelination (Deoni et al., 2011). Magnetization transfer represents an alternative approach to quantify myelin with new approaches refining its modelization by characterizing individually the relaxation and exchange rates of the free water and macromolec...

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“…It was originally created for PD/T2-weighted axially acquired multi-spectral datasets. Enhancements were made to the ImageJ [87] plugin version of this algorithm to handle coronal T1 datasets. This method is modeled for normal subjects and it failed to extract brain containing abnormal anatomic structures.…”

Section: Hybrid Methodsmentioning

confidence: 99%

“…PD/T2-weighted axially acquired multispectral images ImageJ [87] Complex contouring algorithm Coronal T1-weighted images It requires complex contouring algorithm to produce the results. This method is modeled for normal subjects and it failed to extract brain containing abnormal anatomic structures.…”

Section: T1-weighted Imagesmentioning

confidence: 99%

Methods on Skull Stripping of MRI Head Scan Images—a Review

2015

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The high resolution magnetic resonance (MR) brain images contain some non-brain tissues such as skin, fat, muscle, neck, and eye balls compared to the functional images namely positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance imaging (fMRI) which usually contain relatively less non-brain tissues. The presence of these non-brain tissues is considered as a major obstacle for automatic brain image segmentation and analysis techniques. Therefore, quantitative morphometric studies of MR brain images often require a preliminary processing to isolate the brain from extra-cranial or non-brain tissues, commonly referred to as skull stripping. This paper describes the available methods on skull stripping and an exploratory review of recent literature on the existing skull stripping methods.

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Image Processing

Cited by 862 publications

References 94 publications

Worms under Pressure: Bulk Mechanical Properties of C. elegans Are Independent of the Cuticle

Worms under Pressure: Bulk Mechanical Properties of C. elegans Are Independent of the Cuticle

In vivo assessment of myelination by phase imaging at high magnetic field

Methods on Skull Stripping of MRI Head Scan Images—a Review

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