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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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A 3D atlas of neurite tracts reconstructed from aligned GAL4 patterns. (a) 269 stereotyped neurite tracts and their distribution in the brain. The width of each tract equals the respective spatial deviation. The tracts are color-coded randomly for better visualization. Scale bar: 100 µm. (b) Distribution of the spatial deviation of the neurite tracts.
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Figure 6: A 3D atlas of neurite tracts reconstructed from aligned GAL4 patterns. (a) 269 stereotyped neurite tracts and their distribution in the brain. The width of each tract equals the respective spatial deviation. The tracts are color-coded randomly for better visualization. Scale bar: 100 µm. (b) Distribution of the spatial deviation of the neurite tracts.

Mentions: We examined the stereotypy of 269 neurite tracts that project throughout all brain compartments. We reconstructed each tract from at least two aligned brains of each GAL4 line. The spatial variations were computed and used as the width of each tract in visualization (Fig. 6a and Supplementary Video 7). The average variation was 1.98±0.83 µm (Fig. 6b), consistent with our previous independent test of 111 tracts21. This range of variation is within the upper bound of biological stereotypy of the neurite tracts themselves and noise introduced in sample preparation, imaging, and image analysis including registration and tracing. The tracing error was close to 021. Compared to the typical size of an adult fly brain (590 µm × 340 µm × 120 µm), this small variation indicates strong stereotypy of the neurite tracts.


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)

A 3D atlas of neurite tracts reconstructed from aligned GAL4 patterns. (a) 269 stereotyped neurite tracts and their distribution in the brain. The width of each tract equals the respective spatial deviation. The tracts are color-coded randomly for better visualization. Scale bar: 100 µm. (b) Distribution of the spatial deviation of the neurite tracts.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3104101&req=5

Figure 6: A 3D atlas of neurite tracts reconstructed from aligned GAL4 patterns. (a) 269 stereotyped neurite tracts and their distribution in the brain. The width of each tract equals the respective spatial deviation. The tracts are color-coded randomly for better visualization. Scale bar: 100 µm. (b) Distribution of the spatial deviation of the neurite tracts.
Mentions: We examined the stereotypy of 269 neurite tracts that project throughout all brain compartments. We reconstructed each tract from at least two aligned brains of each GAL4 line. The spatial variations were computed and used as the width of each tract in visualization (Fig. 6a and Supplementary Video 7). The average variation was 1.98±0.83 µm (Fig. 6b), consistent with our previous independent test of 111 tracts21. This range of variation is within the upper bound of biological stereotypy of the neurite tracts themselves and noise introduced in sample preparation, imaging, and image analysis including registration and tracing. The tracing error was close to 021. Compared to the typical size of an adult fly brain (590 µm × 340 µm × 120 µm), this small variation indicates strong stereotypy of the neurite tracts.

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