ZENAIDA ALMODOVARNIXON ELEMENTARY SCHOOL

4TH GRADE TEACHERRET - 2013

MENTOR: KEVIN TANGEN

IMAGE RECONSTRUCTION

University of Illinois at Chicago Laboratory for Product and Process Design

East Campus Room 4052Director: Dr. Andreas Linninger

August 13, 2013

ABSTRACT The aim of this study is to compare the cerebrospinal fluid

spaces of the normal rabbit and hydrocephalus model and to compare the volume changes using image reconstruction software applications.

This study employed both manual and automated segmentation methods, in-vivo and ex-vivo to perform 3-D reconstruction of the ventricular system.

The goal of the study is to reveal the normal and hydrocephalus SAS using these software applications and use these findings to improve the treatment of hydrocephalus.

Imaging modalities, 3-D angiography and MRI, in conjunction with image reconstruction contribute to the analysis of hydrocephalus research. There are challenges still to be tackled for the tissue preparation and image acquisition of small animal ex-vivo MRI.

ImageJ and MIMICS are powerful image processing tools which can be used to analyze and understanding how the brain responds to a hydrocephalus state.

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MOTIVATION

GOALS RELEVANCE OF OUR RESEARCH

1. To measure the volume of the ventricular system of a normal rabbit between a hydrocephalus model

2. To create 3-D Medical Image reconstruction of the rabbit’s subarachnoid spaces and central nervous system

3. To generate the basic technical and experimental procedures of the MRI for small animals ex-vivo

To utilize the volume mesh as a mean to qualify the differences of the normal rabbit with a hydrocephalus model.

To perform ex vivo on brain slice preparations

To get a better brain image

To understand the issues and challenges related to small animal MRI experiment including design, data acquisition, and processing.

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MY RESEARCH GOAL MIMICS V. 15.01

Imaging Reconstruction Flow Chart

Medical Images

Segmentation Masks

3 D Object

Surface Mesh

Volume Mesh

Computational Dynamic Flow

Simulation

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MEDICAL IMAGESCREATION OF A SEGMENTATION MASK

Figure 1: MRI image showing an axial slice of the rat CNS 5

Figure 2: MRI image showing an axial slice of the rat CNS with the segmentation masks corresponding to

CSF space (pink) and CNS tissue regions (blue)

7/24/2013The parameters used for obtaining the MRI images on a 9.4T animal MR scanner (Agilent) were as

indicated: Tr =2800ms, Te =16.38ms, averages =2, matrix =256x256, slices =15, Thickness =0.195mm, gap =0mm, orientation: axial

Figure 3: Screenshot of the 3D of the CSF space of the rat

Figure 4: MRI image showing an axial slice of the rat CNS with the segmentation masks corresponding to CSF space

(pink) and CNS tissue regions (blue)

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Mask AMid spine to the end of the spinal canal region

Mask BUpper brain to mid spine

region

SURFACE MESH

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Figure 5 Figure 6

VOLUME MESH

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BOOLEAN SUBTRACTIONDIGITAL SUBTRACTION ANGIOGRAPHY

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Figure 8: Subtracted surface mesh obtained by Boolean subtraction of meshes corresponding to CNS space and CNS tissue.

CNS SAS =

CNStissue

Central Nervous System

GOAL 2: MAGNETIC RESONANCE MICROSCOPY - NEXT STEPS

Definition Figure 9: Brain ex-vivo and a photograph of a brain coronal plane.

Magnetic resonance imaging (MRI)

A technique whereby the interior of the tissue can be accurately imaged; involves the interaction between radio waves and a strong magnetic field.

MR Microscopy can resolve volumes of down to 50 mm³ (clinical MR does 1mm³) use for small animal experiments (in place of destructive histology)

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RESULTS

An angiography image of the experimental set-up.

Dr. Basati induced hydrocephalus with a butterfly needle

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RESULTS

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Brain Model Results of the hydrocephalus rabbit

Image Reconstruction in rat’sCNSHydrocephalus has not produced in rabbits.Digital Subtraction AngiographyNext steps:To understand the issues and Challenges related to small MRI experiment including design, data acquisition and processing.

CONCLUSION 8/7/2013-Next Steps

To utilize the volume measurement as a mean to qualify the differences of the normal rabbit with a hydrocephalus model.

To observe an underlying hydrocephalic rabbit ‘s soft-tissue brain model

To understand the issues and challenges related to small animal MRI experiment including design, data acquisition, and processing.

To understand what is 3-D rotational angiography To generate my final report, video and poster

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REFERENCES Abstract ID: 9970 Title: Small Animal Magnetic Resonance Imaging: Current Trends,

Challenges and Perspectives for Pathological Imaging. Benveniste H. Blackband S. 2002. MR microscopy and high resolution small animal MRI:

Applications in neuroscience research. Prog Neurobiol 67: 393-420. Budinger, T.F. Lauterbur, P.C., 1984. Nuclear magnetic resonance technology for medical

studies. Science 226, 288-298. D’Arceuil H. Liu, C., Levitt, P. Thompson, B., Kosofsky, Crespigny, A. 2007. Three-

dimensional high-resolution diffusion tensor imaging and tractography of the developing rabbit brain. Dev Neurosci 30, 262-275

Driehuy B., Nouls J., Badea A., Bucholz, E., Ghaghada K., Petiet A., and Laurence W. Hedlund L. W. 2008. Small animal imaging with magnetic resonance microscopy. Volume 49, 1. 35-53

MRI Physics 1: Image Acquisition Description: Increases signal/noise: antenna ... Felix Block and Edward Purcell ... Purcell. 6. How fast do

hydrogen atoms spin? Field Strength (Tesla) 180. 40. 1.0. 4.0 ... – PowerPoint PPT presentation http://www.loni.ucla.edu/MAP

This website provides information on digital web based mouse brain atlases that are based on MR microscopy data.

http://mouseatlas.caltech.edu/13.5 pc/ This website provide another mouse brain atlas.

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