Limits...
2D map projections for visualization and quantitative analysis of 3D fluorescence micrographs.

Sendra GH, Hoerth CH, Wunder C, Lorenz H - Sci Rep (2015)

Bottom Line: We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps.Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map.We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles.

View Article: PubMed Central - PubMed

Affiliation: Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.

ABSTRACT
We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map. We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles. Map3-2D software is available at http://www.zmbh.uni-heidelberg.de//Central_Services/Imaging_Facility/Map3-2D.html.

No MeSH data available.


Related in: MedlinePlus

Schematic representation of the of Map3-2D software application.Fluorescence microscopy 3D (up to 5D) image stacks (left) serve as input for the Map3-2D software (middle). The whole surface data of the object of interest is projected onto a 2D map image (right). Map3-2D software registers all pixel information of the image stack (intensity, position within the stack, position with respect to the reference ellipsoid). Regions of interest corresponding to single (blue lines) or multiple layers (orange lines) of the image stack can be selected on the map projection for cross-referencing and quantitative analysis on the original data, and vice versa.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4513544&req=5

f1: Schematic representation of the of Map3-2D software application.Fluorescence microscopy 3D (up to 5D) image stacks (left) serve as input for the Map3-2D software (middle). The whole surface data of the object of interest is projected onto a 2D map image (right). Map3-2D software registers all pixel information of the image stack (intensity, position within the stack, position with respect to the reference ellipsoid). Regions of interest corresponding to single (blue lines) or multiple layers (orange lines) of the image stack can be selected on the map projection for cross-referencing and quantitative analysis on the original data, and vice versa.

Mentions: In order to perform spatial imaging in light microscopy three dimensions need to be considered, which are the lateral (X and Y) and axial (Z) dimensions1. For displaying such 3D image data (e.g. from confocal Z-series), stacks of 2D images that show one image at a time, or 2D projections (of the maximum, sum, mean intensities, or texture-based volume renderings, surfaces or orthoslices) are usually presented. A third option is the use of image galleries, which put a collection of images next to each other in form of a single rather disconnected montage. While all of the abovementioned presentation methods have their advantages, they all fail to display the full 3D surface information content as a single, structurally connected 2D image (Supplementary Fig. 1). As a consequence, there is always some image content that remains absent, lost or altered with any of these display options. Since this is presenting a particular challenge for qualitative and quantitative analyses of structurally connected, multiple images-spanning signals, we sought to overcome such limitations. We developed a new software application in MATLAB (MathWorks), called ‘Map3-2D’, to visualize surface data from 3D fluorescence microscopy. We implemented map projection algorithms used in cartography to unfold spatial fluorescence image data onto a single structurally connected map (Fig. 1). A similar approach has recently been published in order to reduce data rate in storage-demanding selective-plane illumination microscopy of Zebrafish embryos2. Here, we extent the application range of map projections to quantitative analyses of commonly used (and often smaller-scale) translucent biological samples like cells and subcellular components. Our goal was to develop a software that fulfills the following criteria for map projections: (a) the visualization of 3D fluorescence microscopy data not only for spherical and ellipsoidal surfaces, but also for relatively uneven surfaces containing indentations and protrusions, (b) the option to select regions of interest on the map for further quantification and analysis by cross-referencing with the original 3D image data, (c) the implementation of the time (t) dimension, to evaluate dynamic 3D processes, and (d) the presentation of a ready-to-use software as a platform-independent stand-alone application, free of charge, to everybody who is interested, without the need of a programming background.


2D map projections for visualization and quantitative analysis of 3D fluorescence micrographs.

Sendra GH, Hoerth CH, Wunder C, Lorenz H - Sci Rep (2015)

Schematic representation of the of Map3-2D software application.Fluorescence microscopy 3D (up to 5D) image stacks (left) serve as input for the Map3-2D software (middle). The whole surface data of the object of interest is projected onto a 2D map image (right). Map3-2D software registers all pixel information of the image stack (intensity, position within the stack, position with respect to the reference ellipsoid). Regions of interest corresponding to single (blue lines) or multiple layers (orange lines) of the image stack can be selected on the map projection for cross-referencing and quantitative analysis on the original data, and vice versa.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4513544&req=5

f1: Schematic representation of the of Map3-2D software application.Fluorescence microscopy 3D (up to 5D) image stacks (left) serve as input for the Map3-2D software (middle). The whole surface data of the object of interest is projected onto a 2D map image (right). Map3-2D software registers all pixel information of the image stack (intensity, position within the stack, position with respect to the reference ellipsoid). Regions of interest corresponding to single (blue lines) or multiple layers (orange lines) of the image stack can be selected on the map projection for cross-referencing and quantitative analysis on the original data, and vice versa.
Mentions: In order to perform spatial imaging in light microscopy three dimensions need to be considered, which are the lateral (X and Y) and axial (Z) dimensions1. For displaying such 3D image data (e.g. from confocal Z-series), stacks of 2D images that show one image at a time, or 2D projections (of the maximum, sum, mean intensities, or texture-based volume renderings, surfaces or orthoslices) are usually presented. A third option is the use of image galleries, which put a collection of images next to each other in form of a single rather disconnected montage. While all of the abovementioned presentation methods have their advantages, they all fail to display the full 3D surface information content as a single, structurally connected 2D image (Supplementary Fig. 1). As a consequence, there is always some image content that remains absent, lost or altered with any of these display options. Since this is presenting a particular challenge for qualitative and quantitative analyses of structurally connected, multiple images-spanning signals, we sought to overcome such limitations. We developed a new software application in MATLAB (MathWorks), called ‘Map3-2D’, to visualize surface data from 3D fluorescence microscopy. We implemented map projection algorithms used in cartography to unfold spatial fluorescence image data onto a single structurally connected map (Fig. 1). A similar approach has recently been published in order to reduce data rate in storage-demanding selective-plane illumination microscopy of Zebrafish embryos2. Here, we extent the application range of map projections to quantitative analyses of commonly used (and often smaller-scale) translucent biological samples like cells and subcellular components. Our goal was to develop a software that fulfills the following criteria for map projections: (a) the visualization of 3D fluorescence microscopy data not only for spherical and ellipsoidal surfaces, but also for relatively uneven surfaces containing indentations and protrusions, (b) the option to select regions of interest on the map for further quantification and analysis by cross-referencing with the original 3D image data, (c) the implementation of the time (t) dimension, to evaluate dynamic 3D processes, and (d) the presentation of a ready-to-use software as a platform-independent stand-alone application, free of charge, to everybody who is interested, without the need of a programming background.

Bottom Line: We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps.Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map.We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles.

View Article: PubMed Central - PubMed

Affiliation: Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.

ABSTRACT
We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map. We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles. Map3-2D software is available at http://www.zmbh.uni-heidelberg.de//Central_Services/Imaging_Facility/Map3-2D.html.

No MeSH data available.


Related in: MedlinePlus