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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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Stereotypy of neuronal morphology and reproducibility of GAL4 expression patterns. (a) Two aligned and overlaid examples (magenta and green) of the a278-GAL4 expression pattern, from different brains. Scale bar: 20 µm. (b) 3D reconstruction of the major neurite tracts in (a). Magenta and green, surface representations of the reconstructed tracts. Gray, GAL4 pattern. Scale bar: 20 µm. (c) 3D reconstructed neurite tracts (gray) from 20 aligned a278-GAL4 images, along with their mean tract model (red). (d) Average deviation of the mean tract model from each reconstructed tract.
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Figure 3: Stereotypy of neuronal morphology and reproducibility of GAL4 expression patterns. (a) Two aligned and overlaid examples (magenta and green) of the a278-GAL4 expression pattern, from different brains. Scale bar: 20 µm. (b) 3D reconstruction of the major neurite tracts in (a). Magenta and green, surface representations of the reconstructed tracts. Gray, GAL4 pattern. Scale bar: 20 µm. (c) 3D reconstructed neurite tracts (gray) from 20 aligned a278-GAL4 images, along with their mean tract model (red). (d) Average deviation of the mean tract model from each reconstructed tract.

Mentions: The variation between individual aligned brains of the same genotype is a combination of biological difference, variation introduced during sample preparation or imaging, and alignment error. In a previous study11, the variance of axon position was estimated to be approximately 2.5 ~ 4.3µm in the inner antennal cerebral tract (iACT) and at its neurite bifurcation point. We addressed a similar question by aligning 20 samples of a278-GAL4; UAS-mCD8-GFP to the common target TA. The large neurite bundles in aligned samples (Fig. 3a) were traced in 3D (Fig. 3b) using V3D-Neuron21,22. A mean tract model, Rm, of all these tracts was computed (Fig. 3c, and Supplementary Video 2). The neurite tracts were compared to Rm, at 243 evenly spaced locations. The variability of tract position was 3.26 µm (about 5.6 voxels in our images) with a range of 2.1 to 5.1 µm (Fig. 3d).


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)

Stereotypy of neuronal morphology and reproducibility of GAL4 expression patterns. (a) Two aligned and overlaid examples (magenta and green) of the a278-GAL4 expression pattern, from different brains. Scale bar: 20 µm. (b) 3D reconstruction of the major neurite tracts in (a). Magenta and green, surface representations of the reconstructed tracts. Gray, GAL4 pattern. Scale bar: 20 µm. (c) 3D reconstructed neurite tracts (gray) from 20 aligned a278-GAL4 images, along with their mean tract model (red). (d) Average deviation of the mean tract model from each reconstructed tract.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3104101&req=5

Figure 3: Stereotypy of neuronal morphology and reproducibility of GAL4 expression patterns. (a) Two aligned and overlaid examples (magenta and green) of the a278-GAL4 expression pattern, from different brains. Scale bar: 20 µm. (b) 3D reconstruction of the major neurite tracts in (a). Magenta and green, surface representations of the reconstructed tracts. Gray, GAL4 pattern. Scale bar: 20 µm. (c) 3D reconstructed neurite tracts (gray) from 20 aligned a278-GAL4 images, along with their mean tract model (red). (d) Average deviation of the mean tract model from each reconstructed tract.
Mentions: The variation between individual aligned brains of the same genotype is a combination of biological difference, variation introduced during sample preparation or imaging, and alignment error. In a previous study11, the variance of axon position was estimated to be approximately 2.5 ~ 4.3µm in the inner antennal cerebral tract (iACT) and at its neurite bifurcation point. We addressed a similar question by aligning 20 samples of a278-GAL4; UAS-mCD8-GFP to the common target TA. The large neurite bundles in aligned samples (Fig. 3a) were traced in 3D (Fig. 3b) using V3D-Neuron21,22. A mean tract model, Rm, of all these tracts was computed (Fig. 3c, and Supplementary Video 2). The neurite tracts were compared to Rm, at 243 evenly spaced locations. The variability of tract position was 3.26 µm (about 5.6 voxels in our images) with a range of 2.1 to 5.1 µm (Fig. 3d).

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