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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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Comparison of computational alignment of separate brains with co-expression within the same brain. For all images, grey shows N-cadherin (N-Cad) labeling, which serves as the reference signal for alignment to the nc82-labeled target. Magenta, FasII antibody staining; green, GAL4 expression pattern (anti-GFP stain). (a) Wild-type w1118 adult brain. (b–d) Expression patterns of the indicated lines shown as maximum intensity projections of 20X confocal image stacks. (e, g, i) Cross-sectional views of computational alignments of FasII expression from (a) with GAL4 patterns from (b–d). (f, h, j) Matched cross-sectional views of brains expressing the GAL4 lines and labeled with both anti-GFP and anti-FasII to show biological co-localization. OK107 and 201Y expression patterns overlap with FasII (yellow arrows), but C232 expresses in adjacent but non-overlapping brain regions (red arrow). Scale bars, 100 µm.
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Figure 5: Comparison of computational alignment of separate brains with co-expression within the same brain. For all images, grey shows N-cadherin (N-Cad) labeling, which serves as the reference signal for alignment to the nc82-labeled target. Magenta, FasII antibody staining; green, GAL4 expression pattern (anti-GFP stain). (a) Wild-type w1118 adult brain. (b–d) Expression patterns of the indicated lines shown as maximum intensity projections of 20X confocal image stacks. (e, g, i) Cross-sectional views of computational alignments of FasII expression from (a) with GAL4 patterns from (b–d). (f, h, j) Matched cross-sectional views of brains expressing the GAL4 lines and labeled with both anti-GFP and anti-FasII to show biological co-localization. OK107 and 201Y expression patterns overlap with FasII (yellow arrows), but C232 expresses in adjacent but non-overlapping brain regions (red arrow). Scale bars, 100 µm.

Mentions: We performed an independent test of BrainAligner’s accuracy by comparing the computational alignment and co-labeling for FasII antibody staining, which labels the mushroom bodies, and various GAL4 lines that express in or near the mushroom bodies. BrainAligner accurately predicted the overlap of FasII antibody staining with the 201Y and OK107-GAL4 patterns, while C232-GAL4, which expresses in the central complex, does not co-localize with FasII (Figure 5).


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)

Comparison of computational alignment of separate brains with co-expression within the same brain. For all images, grey shows N-cadherin (N-Cad) labeling, which serves as the reference signal for alignment to the nc82-labeled target. Magenta, FasII antibody staining; green, GAL4 expression pattern (anti-GFP stain). (a) Wild-type w1118 adult brain. (b–d) Expression patterns of the indicated lines shown as maximum intensity projections of 20X confocal image stacks. (e, g, i) Cross-sectional views of computational alignments of FasII expression from (a) with GAL4 patterns from (b–d). (f, h, j) Matched cross-sectional views of brains expressing the GAL4 lines and labeled with both anti-GFP and anti-FasII to show biological co-localization. OK107 and 201Y expression patterns overlap with FasII (yellow arrows), but C232 expresses in adjacent but non-overlapping brain regions (red arrow). Scale bars, 100 µm.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3104101&req=5

Figure 5: Comparison of computational alignment of separate brains with co-expression within the same brain. For all images, grey shows N-cadherin (N-Cad) labeling, which serves as the reference signal for alignment to the nc82-labeled target. Magenta, FasII antibody staining; green, GAL4 expression pattern (anti-GFP stain). (a) Wild-type w1118 adult brain. (b–d) Expression patterns of the indicated lines shown as maximum intensity projections of 20X confocal image stacks. (e, g, i) Cross-sectional views of computational alignments of FasII expression from (a) with GAL4 patterns from (b–d). (f, h, j) Matched cross-sectional views of brains expressing the GAL4 lines and labeled with both anti-GFP and anti-FasII to show biological co-localization. OK107 and 201Y expression patterns overlap with FasII (yellow arrows), but C232 expresses in adjacent but non-overlapping brain regions (red arrow). Scale bars, 100 µm.
Mentions: We performed an independent test of BrainAligner’s accuracy by comparing the computational alignment and co-labeling for FasII antibody staining, which labels the mushroom bodies, and various GAL4 lines that express in or near the mushroom bodies. BrainAligner accurately predicted the overlap of FasII antibody staining with the 201Y and OK107-GAL4 patterns, while C232-GAL4, which expresses in the central complex, does not co-localize with FasII (Figure 5).

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