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BrainAligner: 3D registration atlases of Drosophila brains.

Peng H, Chung P, Long F, Qu L, Jenett A, Seeds AM, Myers EW, Simpson JH - Nat. Methods (2011)

Bottom Line: Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology.Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain.We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

View Article: PubMed Central - PubMed

Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA. pengh@janelia.hhmi.org

ABSTRACT
Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology. Given a target brain labeled with predefined landmarks, the BrainAligner program automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain. We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

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BrainAligner registers images of neurons from different brains onto a common coordinate system. (a–b) Maximum intensity projections of confocal images of a64-GAL4 and a74-GAL4 brains. Neurons are visualized by membrane-targeted GFP and brain morphology is visualized by staining with the antibody nc82. (c) Aligned and overlaid neuronal patterns of (a) and (b). (d) Alignment of many GAL4 expression patterns. Patterns of interest can be selected and displayed in the common coordinate system. R1 and R2, regions of interest. (e) V3D-AtlasViewer software for viewing the 3D pattern atlas. (f–h) Zoomed-in single-section views of R1 and R2 in (d). Scale bars in all sub-figures: 50 µm.
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Figure 1: BrainAligner registers images of neurons from different brains onto a common coordinate system. (a–b) Maximum intensity projections of confocal images of a64-GAL4 and a74-GAL4 brains. Neurons are visualized by membrane-targeted GFP and brain morphology is visualized by staining with the antibody nc82. (c) Aligned and overlaid neuronal patterns of (a) and (b). (d) Alignment of many GAL4 expression patterns. Patterns of interest can be selected and displayed in the common coordinate system. R1 and R2, regions of interest. (e) V3D-AtlasViewer software for viewing the 3D pattern atlas. (f–h) Zoomed-in single-section views of R1 and R2 in (d). Scale bars in all sub-figures: 50 µm.

Mentions: BrainAligner registers 3D images of adult Drosophila brain into a common coordinate system (Fig. 1). Brains that express GFP in various neural subsets were dissected and labeled with an antibody to GFP (colors in Fig. 1a–b); this is the pattern channel. Brains were also labeled with nc82, an antibody that detects a ubiquitous presynaptic component and marks the entire synaptic neuropil17 (gray in Fig. 1a–b); this is the reference channel. The brains to be registered have different orientations, sizes, and morphological deformations that are either biological or introduced in sample preparation. For each subject brain, BrainAligner maps the reference channel to a standardized target brain image using a nonlinear geometrical warp. Using the same transformation, the pattern channel from the subject image is then warped onto the target. Multiple subject images are aligned to a common target so that their patterns can be compared in the same coordinate space (Fig. 1c and Supplementary Video 1). In this way, we have mapped a large collection of GAL4 patterns into a common framework to identify intersecting expression patterns in various anatomical structures (Fig. 1d–h and Supplementary Video 2).


BrainAligner: 3D registration atlases of Drosophila brains.

Peng H, Chung P, Long F, Qu L, Jenett A, Seeds AM, Myers EW, Simpson JH - Nat. Methods (2011)

BrainAligner registers images of neurons from different brains onto a common coordinate system. (a–b) Maximum intensity projections of confocal images of a64-GAL4 and a74-GAL4 brains. Neurons are visualized by membrane-targeted GFP and brain morphology is visualized by staining with the antibody nc82. (c) Aligned and overlaid neuronal patterns of (a) and (b). (d) Alignment of many GAL4 expression patterns. Patterns of interest can be selected and displayed in the common coordinate system. R1 and R2, regions of interest. (e) V3D-AtlasViewer software for viewing the 3D pattern atlas. (f–h) Zoomed-in single-section views of R1 and R2 in (d). Scale bars in all sub-figures: 50 µm.
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Related In: Results  -  Collection

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Figure 1: BrainAligner registers images of neurons from different brains onto a common coordinate system. (a–b) Maximum intensity projections of confocal images of a64-GAL4 and a74-GAL4 brains. Neurons are visualized by membrane-targeted GFP and brain morphology is visualized by staining with the antibody nc82. (c) Aligned and overlaid neuronal patterns of (a) and (b). (d) Alignment of many GAL4 expression patterns. Patterns of interest can be selected and displayed in the common coordinate system. R1 and R2, regions of interest. (e) V3D-AtlasViewer software for viewing the 3D pattern atlas. (f–h) Zoomed-in single-section views of R1 and R2 in (d). Scale bars in all sub-figures: 50 µm.
Mentions: BrainAligner registers 3D images of adult Drosophila brain into a common coordinate system (Fig. 1). Brains that express GFP in various neural subsets were dissected and labeled with an antibody to GFP (colors in Fig. 1a–b); this is the pattern channel. Brains were also labeled with nc82, an antibody that detects a ubiquitous presynaptic component and marks the entire synaptic neuropil17 (gray in Fig. 1a–b); this is the reference channel. The brains to be registered have different orientations, sizes, and morphological deformations that are either biological or introduced in sample preparation. For each subject brain, BrainAligner maps the reference channel to a standardized target brain image using a nonlinear geometrical warp. Using the same transformation, the pattern channel from the subject image is then warped onto the target. Multiple subject images are aligned to a common target so that their patterns can be compared in the same coordinate space (Fig. 1c and Supplementary Video 1). In this way, we have mapped a large collection of GAL4 patterns into a common framework to identify intersecting expression patterns in various anatomical structures (Fig. 1d–h and Supplementary Video 2).

Bottom Line: Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology.Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain.We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

View Article: PubMed Central - PubMed

Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA. pengh@janelia.hhmi.org

ABSTRACT
Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology. Given a target brain labeled with predefined landmarks, the BrainAligner program automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain. We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

Show MeSH
Related in: MedlinePlus