Limits...
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.

Show MeSH

Related in: MedlinePlus

Expression pattern overlap by computational and biological methods. (a) Maximum intensity projection of a278-GAL4; UAS-mCD8-GFP. Scale bar: 100 µm. (b) Maximum intensity projection of LexAP036; lexop-CD2-GFP. Scale bar: 100 µm. (c) Aligned image of GAL4 and LexA expression patterns in (a) and (b), with a zoomed-in view to the right. Scale bar: 50 µm. (d) Co-expression of the GAL4 and LexA patterns, with a zoomed-in view to the right. Scale bar: 50 µm. Arrows indicate the 11 locations where colocalization of the two patterns was measured; the yellow arrow indicates a region of substantial overlap. (e–f) Cross-sectional views of single slices of the aligned (e) and co-expressed (f) samples at a position corresponding to the yellow arrow in (c) and (d). Scale bars: 25 µm.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3104101&req=5

Figure 4: Expression pattern overlap by computational and biological methods. (a) Maximum intensity projection of a278-GAL4; UAS-mCD8-GFP. Scale bar: 100 µm. (b) Maximum intensity projection of LexAP036; lexop-CD2-GFP. Scale bar: 100 µm. (c) Aligned image of GAL4 and LexA expression patterns in (a) and (b), with a zoomed-in view to the right. Scale bar: 50 µm. (d) Co-expression of the GAL4 and LexA patterns, with a zoomed-in view to the right. Scale bar: 50 µm. Arrows indicate the 11 locations where colocalization of the two patterns was measured; the yellow arrow indicates a region of substantial overlap. (e–f) Cross-sectional views of single slices of the aligned (e) and co-expressed (f) samples at a position corresponding to the yellow arrow in (c) and (d). Scale bars: 25 µm.

Mentions: With ~3µm variance, BrainAligner produces reliable results. We further differentiated biological variability from aligner variance. The existence of two binary expression systems, GAL4 and LexA23, permits rigorous comparison of a computational prediction of overlap with a biological test of co-expression. The LexA line (LexAP036) showed potential overlap with the a278-GAL4 line used above in the Ω-shaped antennal lobe commissure (ALC) (Fig. 4a and 4b) when registered with BrainAligner (Fig. 4c and 4e). We then co-expressed distinct reporter constructs using the LexA and GAL4 systems simultaneously in the same fly and showed that there is indeed overlapping expression in the ALC (Fig. 4d and 4f). We estimated the precision of BrainAligner’s registration using the absolute value of the difference of the biological spatial distance of co-localized patterns and their respective spatial distance measured from the computationally aligned patterns. The average distance measured at 11 different spatial locations (Fig. 4d) along ALC of the aligned patterns and physically overlapping patterns was 1.8±1.1µm. Therefore the estimated registration precision was 0.8 to 2.9 µm. We also saw agreement between the aligned and co-expressed images of other GAL4-LexA pairs with expression patterns in the optic tubercle (Supplementary Fig. 4, Supplementary Videos 4a–b).


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)

Expression pattern overlap by computational and biological methods. (a) Maximum intensity projection of a278-GAL4; UAS-mCD8-GFP. Scale bar: 100 µm. (b) Maximum intensity projection of LexAP036; lexop-CD2-GFP. Scale bar: 100 µm. (c) Aligned image of GAL4 and LexA expression patterns in (a) and (b), with a zoomed-in view to the right. Scale bar: 50 µm. (d) Co-expression of the GAL4 and LexA patterns, with a zoomed-in view to the right. Scale bar: 50 µm. Arrows indicate the 11 locations where colocalization of the two patterns was measured; the yellow arrow indicates a region of substantial overlap. (e–f) Cross-sectional views of single slices of the aligned (e) and co-expressed (f) samples at a position corresponding to the yellow arrow in (c) and (d). Scale bars: 25 µm.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Expression pattern overlap by computational and biological methods. (a) Maximum intensity projection of a278-GAL4; UAS-mCD8-GFP. Scale bar: 100 µm. (b) Maximum intensity projection of LexAP036; lexop-CD2-GFP. Scale bar: 100 µm. (c) Aligned image of GAL4 and LexA expression patterns in (a) and (b), with a zoomed-in view to the right. Scale bar: 50 µm. (d) Co-expression of the GAL4 and LexA patterns, with a zoomed-in view to the right. Scale bar: 50 µm. Arrows indicate the 11 locations where colocalization of the two patterns was measured; the yellow arrow indicates a region of substantial overlap. (e–f) Cross-sectional views of single slices of the aligned (e) and co-expressed (f) samples at a position corresponding to the yellow arrow in (c) and (d). Scale bars: 25 µm.
Mentions: With ~3µm variance, BrainAligner produces reliable results. We further differentiated biological variability from aligner variance. The existence of two binary expression systems, GAL4 and LexA23, permits rigorous comparison of a computational prediction of overlap with a biological test of co-expression. The LexA line (LexAP036) showed potential overlap with the a278-GAL4 line used above in the Ω-shaped antennal lobe commissure (ALC) (Fig. 4a and 4b) when registered with BrainAligner (Fig. 4c and 4e). We then co-expressed distinct reporter constructs using the LexA and GAL4 systems simultaneously in the same fly and showed that there is indeed overlapping expression in the ALC (Fig. 4d and 4f). We estimated the precision of BrainAligner’s registration using the absolute value of the difference of the biological spatial distance of co-localized patterns and their respective spatial distance measured from the computationally aligned patterns. The average distance measured at 11 different spatial locations (Fig. 4d) along ALC of the aligned patterns and physically overlapping patterns was 1.8±1.1µm. Therefore the estimated registration precision was 0.8 to 2.9 µm. We also saw agreement between the aligned and co-expressed images of other GAL4-LexA pairs with expression patterns in the optic tubercle (Supplementary Fig. 4, Supplementary Videos 4a–b).

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