- Title
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A 3D adult zebrafish brain atlas (AZBA) for the digital age
- Authors
- Kenney, J.W., Steadman, P.E., Young, O., Shi, M.T., Polanco, M., Dubaishi, S., Covert, K., Mueller, T., Frankland, P.W.
- Source
- Full text @ Elife
Dissected brain samples were first subject to staining and tissue clearing. This was followed by whole-mount imaging using light-sheet fluorescence microscopy. Three-dimensional volumes were created from individual image sets, and then registered into the same anatomical space prior to averaging to generate a representative image. Finally, volumes were segmented into over 200 neuroanatomical regions.
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(A) Image of adult zebrafish brain samples before (top) and after (bottom) clearing using iDISCO+. (B) Example TO-PRO-stained images from a single sample acquired in the horizontal plane during light-sheet imaging. (C) Three-dimensional volumes generated from a set of light-sheet images from an individual brain visualized using a maximum intensity projection (left) and exterior volume (right). (D) Coronal (left) and sagittal (right) views of an individual brain generated from a single three-dimensional volume.
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(A) Raw TO-PRO images from 17 fish were first aligned using linear transformations (LSQ6 and LSQ12) followed by a final nonlinear transformation (right). Deformation grids at each stage are overlaid. Consensus average images at each stage of the pipeline are given below. (B) Raw autofluorescence images (top) acquired at the same time as the TO-PRO images were registered into the same space using the transformations derived from TO-PRO registration (middle). Images were then averaged together to generate a corresponding autofluorescence average in the same anatomical space as the TO-PRO images (bottom).
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(A) Representative light-sheet images taken in the horizontal plane from individual brains stained with indicated antibodies. (B) Autofluorescence images acquired during antibody staining (top) were registered into the same space as autofluorescence images acquired during TO-PRO staining (bottom). (C) Transformations from autofluorescence registration were applied to antibody images to bring antibody stains into the same anatomical space as the TO-PRO stain. Yellow crosshairs are in the same place on each image. (D) Example of correspondence between TO-PRO and antibody images and how stains can be used to identify the boundaries of specific nuclei (green arrow: locus coeruleus) and white matter tracts by a lack of staining (pink arrowhead: medial longitudinal fascicle).
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(A) Averaged and registered TO-PRO images alongside the atlas segmentation. For sagittal (top), horizontal (middle), and coronal (bottom) planes, numbers are distance (in mm) from the midline, top, and anterior-most portion of the brain, respectively. (B, C) Averaged and registered TH and 5-HT-stained images where hotter colors indicate a stronger signal. Numbers same as in (A). Slices in each plane were chosen to show regions containing high levels of staining (see Results for description). (D) Three-dimensional representation of the segmentation with a sagittal and horizontal cutaway overlaid with the TO-PRO stain of the atlas.
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Numbers are distance (in mm) from the anterior-most portion of the brain. |
For sagittal (top) and horizontal (left, bottom), numbers represent distance (in mm) from midline or top of the brain, respectively. Slices for each plane were chosen based on the presence of staining (see Results for description).
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