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Pathology interface for the molecular analysis of tissue by mass spectrometry.

Norris JL, Tsui T, Gutierrez DB, Caprioli RM - J Pathol Inform (2016)

Bottom Line: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology.We describe a microscopy-driven approach to tissue analysis by IMS.The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA.

ABSTRACT

Background: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology. Although IMS technology has matured over recent years, the link between microscopy imaging currently used by pathologists and MS-based molecular imaging has not been established.

Methods: We adapted the Vanderbilt University Tissue Core workflow for IMS into a web-based system that facilitates remote collaboration. The platform was designed to perform within acceptable web response times for viewing, annotating, and processing high resolution microscopy images.

Results: We describe a microscopy-driven approach to tissue analysis by IMS.

Conclusion: The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.

No MeSH data available.


Related in: MedlinePlus

Screenshots from the pathology interface for mass spectrometry interface highlight the software features and workflow. (a) A scanned H and E stained tissue section can be viewed through the image markup screen and examined remotely by a pathologist. (b) The pathologist can then annotate the tissue via a user-defined color palette to distinguish regions of interest, for example, tissue classes (e.g., normal versus disease) or cell types. Annotations can be made as discrete spots (as shown) or regions. (c) Pathology interface for mass spectrometry can zoom to regions of interest. Scale bars and the magnification level are automatically rescaled according to the zoom level. (d) A mass spectrometry spectrum acquired from the spot labeled “1” in panels b and c
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Figure 2: Screenshots from the pathology interface for mass spectrometry interface highlight the software features and workflow. (a) A scanned H and E stained tissue section can be viewed through the image markup screen and examined remotely by a pathologist. (b) The pathologist can then annotate the tissue via a user-defined color palette to distinguish regions of interest, for example, tissue classes (e.g., normal versus disease) or cell types. Annotations can be made as discrete spots (as shown) or regions. (c) Pathology interface for mass spectrometry can zoom to regions of interest. Scale bars and the magnification level are automatically rescaled according to the zoom level. (d) A mass spectrometry spectrum acquired from the spot labeled “1” in panels b and c

Mentions: In contrast, the PIMS interface does not necessitate the transfer of a compressed image to capture the annotations needed to execute the required experiment. After tissue sections are imaged, users upload images to the cloud from which they are automatically imported into the PIMS database, eliminating the need to reduce image size and resolution for E-mail transfer of images. Collaborators can open the PIMS interface through any web browser (Chrome, Firefox, Internet Explorer, Safari, etc.,) and therefore, it can be used on PC or Mac desktops, laptops, or tablets with no additional installs required. Images can be composed – viewed, cropped, rotated, and annotated – using the Image Markup Viewer [Figure 2a-c]. The image server supports layered tiling to optimize performance in viewing large, high-resolution (gigapixel) images so that users can efficiently view and annotate tissue areas. Opening images, this size can take hours on a common laptop/desktop setup, but PIMS accomplishes this task in seconds.


Pathology interface for the molecular analysis of tissue by mass spectrometry.

Norris JL, Tsui T, Gutierrez DB, Caprioli RM - J Pathol Inform (2016)

Screenshots from the pathology interface for mass spectrometry interface highlight the software features and workflow. (a) A scanned H and E stained tissue section can be viewed through the image markup screen and examined remotely by a pathologist. (b) The pathologist can then annotate the tissue via a user-defined color palette to distinguish regions of interest, for example, tissue classes (e.g., normal versus disease) or cell types. Annotations can be made as discrete spots (as shown) or regions. (c) Pathology interface for mass spectrometry can zoom to regions of interest. Scale bars and the magnification level are automatically rescaled according to the zoom level. (d) A mass spectrometry spectrum acquired from the spot labeled “1” in panels b and c
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4837791&req=5

Figure 2: Screenshots from the pathology interface for mass spectrometry interface highlight the software features and workflow. (a) A scanned H and E stained tissue section can be viewed through the image markup screen and examined remotely by a pathologist. (b) The pathologist can then annotate the tissue via a user-defined color palette to distinguish regions of interest, for example, tissue classes (e.g., normal versus disease) or cell types. Annotations can be made as discrete spots (as shown) or regions. (c) Pathology interface for mass spectrometry can zoom to regions of interest. Scale bars and the magnification level are automatically rescaled according to the zoom level. (d) A mass spectrometry spectrum acquired from the spot labeled “1” in panels b and c
Mentions: In contrast, the PIMS interface does not necessitate the transfer of a compressed image to capture the annotations needed to execute the required experiment. After tissue sections are imaged, users upload images to the cloud from which they are automatically imported into the PIMS database, eliminating the need to reduce image size and resolution for E-mail transfer of images. Collaborators can open the PIMS interface through any web browser (Chrome, Firefox, Internet Explorer, Safari, etc.,) and therefore, it can be used on PC or Mac desktops, laptops, or tablets with no additional installs required. Images can be composed – viewed, cropped, rotated, and annotated – using the Image Markup Viewer [Figure 2a-c]. The image server supports layered tiling to optimize performance in viewing large, high-resolution (gigapixel) images so that users can efficiently view and annotate tissue areas. Opening images, this size can take hours on a common laptop/desktop setup, but PIMS accomplishes this task in seconds.

Bottom Line: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology.We describe a microscopy-driven approach to tissue analysis by IMS.The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA.

ABSTRACT

Background: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology. Although IMS technology has matured over recent years, the link between microscopy imaging currently used by pathologists and MS-based molecular imaging has not been established.

Methods: We adapted the Vanderbilt University Tissue Core workflow for IMS into a web-based system that facilitates remote collaboration. The platform was designed to perform within acceptable web response times for viewing, annotating, and processing high resolution microscopy images.

Results: We describe a microscopy-driven approach to tissue analysis by IMS.

Conclusion: The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.

No MeSH data available.


Related in: MedlinePlus