Connecting imaging mass spectrometry and magnetic resonance imaging-based anatomical atlases for automated anatomical interpretation and differential analysis

Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information...

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Veröffentlicht in:	Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Jg. 1865; H. 7; S. 967 - 977
Hauptverfasser:	Verbeeck, Nico, Spraggins, Jeffrey M., Murphy, Monika J.M., Wang, Hui-dong, Deutch, Ariel Y., Caprioli, Richard M., Van de Plas, Raf
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Netherlands Elsevier B.V 01.07.2017 Elsevier BV
Schlagworte:	Anatomical atlas animal models Animals biochemical compounds Brain Brain - anatomy & histology Brain - metabolism Brain - pathology FTICR MS image analysis Image Processing, Computer-Assisted Image Processing, Computer-Assisted - methods Imaging mass spectrometry Imaging, Three-Dimensional Imaging, Three-Dimensional - methods Ions Ions - metabolism Magnetic Resonance Imaging Magnetic Resonance Imaging - methods Male Mass Spectrometry Mass Spectrometry - methods Mice MRI Parkinson Disease Parkinson Disease - pathology Rat brain Rats Rats, Sprague-Dawley SBA PD AMBA MRI Imaging mass spectrometry t-SNE FTICR MS FTICR Rat brain PCA Anatomical atlas
ISSN:	1570-9639, 1878-1454
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Abstract	Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model. The measurements are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
AbstractList	Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model. The measurements are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model. The measurements are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model. The measurements are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model. The measurements are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Author	Verbeeck, Nico Wang, Hui-dong Caprioli, Richard M. Van de Plas, Raf Murphy, Monika J.M. Deutch, Ariel Y. Spraggins, Jeffrey M.
Author_xml	– sequence: 1 givenname: Nico surname: Verbeeck fullname: Verbeeck, Nico email: n.verbeeck@tudelft.nl organization: Delft Center for Systems and Control (DCSC), Delft University of Technology, Mekelweg 2, 2628 CD Delft, the Netherlands – sequence: 2 givenname: Jeffrey M. surname: Spraggins fullname: Spraggins, Jeffrey M. email: jeff.spraggins@vanderbilt.edu organization: Mass Spectrometry Research Center (MSRC), Vanderbilt University, 465 21st Ave. South, 9160 Medical Research Building III, Nashville, TN 37240, USA – sequence: 3 givenname: Monika J.M. surname: Murphy fullname: Murphy, Monika J.M. email: monika.murphy@vanderbilt.edu organization: Program in Neuroscience, Vanderbilt University, U-1205 Medical Research Building III, 465 21st Ave. South, Nashville, TN 37232, USA – sequence: 4 givenname: Hui-dong surname: Wang fullname: Wang, Hui-dong email: huidong.wang@vanderbilt.edu organization: Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, 1211 Medical Center Dr. Nashville, TN 37232, USA – sequence: 5 givenname: Ariel Y. surname: Deutch fullname: Deutch, Ariel Y. email: ariel.deutch@vanderbilt.edu organization: Program in Neuroscience, Vanderbilt University, U-1205 Medical Research Building III, 465 21st Ave. South, Nashville, TN 37232, USA – sequence: 6 givenname: Richard M. surname: Caprioli fullname: Caprioli, Richard M. email: richard.m.caprioli@vanderbilt.edu organization: Mass Spectrometry Research Center (MSRC), Vanderbilt University, 465 21st Ave. South, 9160 Medical Research Building III, Nashville, TN 37240, USA – sequence: 7 givenname: Raf surname: Van de Plas fullname: Van de Plas, Raf email: raf.vandeplas@tudelft.nl organization: Delft Center for Systems and Control (DCSC), Delft University of Technology, Mekelweg 2, 2628 CD Delft, the Netherlands
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Snippet	Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it...
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SubjectTerms	Anatomical atlas animal models Animals biochemical compounds Brain Brain - anatomy & histology Brain - metabolism Brain - pathology FTICR MS image analysis Image Processing, Computer-Assisted Image Processing, Computer-Assisted - methods Imaging mass spectrometry Imaging, Three-Dimensional Imaging, Three-Dimensional - methods Ions Ions - metabolism Magnetic Resonance Imaging Magnetic Resonance Imaging - methods Male Mass Spectrometry Mass Spectrometry - methods Mice MRI Parkinson Disease Parkinson Disease - pathology Rat brain Rats Rats, Sprague-Dawley
Title	Connecting imaging mass spectrometry and magnetic resonance imaging-based anatomical atlases for automated anatomical interpretation and differential analysis
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