Dataset Open Access
A 3D Adult Zebrafish Brain Atlas (AZBA) for the Digital Age
Kenney, Justin W.;
Steadman, Patrick E.;
Young, Olivia;
Shi, Meng Ting;
Polanco, Maris;
Dubaishi, Saba;
Covert, Kristopher;
Mueller, Thomas;
Frankland, Paul W.
Zebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the first fully segmented three-dimensional digital adult zebrafish brain atlas (AZBA). AZBA was built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. These images were used to guide segmentation of the atlas into over 200 neuroanatomical regions comprising the entirety of the adult zebrafish brain. As an open source, online (azba.wayne.edu), updatable digital resource, AZBA will significantly enhance the use of adult zebrafish in furthering our understanding of vertebrate brain function in both health and disease.
Images are best viewed using ITK-SNAP:
http://www.itksnap.org/pmwiki/pmwiki.php
Video tutorial: https://youtu.be/uVLqFJd4LDk
Basic usage and viewing after installing and opening ITK-SNAP:
-
File --> Open main image
- Select 20180219_topro_average_2020.nii.gz
- To add the segmentation:
- Segmentation --> Open segmentation
- Select 2021-08-21_zfish_segmentation.nii.gz (or latest segmentation file)
- To add correct labels and colors to the segmentation:
- Segmentation --> Import label description
- Select 2021-08-21_Label_descriptions.txt (or segmentation file with date that matches the segmentation loaded in the previous step)
You can now explore the atlas in the coronal, horizontal, and sagittal planes.
To add an additional image alongside the main image loaded above (e.g., the tyrosine hydroxylase stains):
-
File --> add another image
- Select 20180505_TH_average.nii.gz (or image set of your choice)
- To view images side-by-side you may need to select the "tiled layout":
-
Edit --> Layers --> "Entered tiled layout"
- Alternatively, you can press the "\" key to toggle between layouts
-
Edit --> Layers --> "Entered tiled layout"
Navigating the atlas and segmentation is most easily done using "crosshair mode" (press "1") and/or "zoom/pan mode" (press "2"). These are the first two selections in the top "main toolbar" in the top left corner:
- Mouse wheel allows you to scroll through the image slices
- Right mouse click zooms in/out
- In 'crosshair mode' left mouse click changes location of the crosshair. You can see the abbreviation for the label under the cursor on the left side under "Label under cursor:"
- In 'zoom/pan mode' holding and clicking the left mouse button willl allow to move the images around
Other useful commands:
- "x" will toggle the segmentation
- "c" will center the images to the location of the crosshair in all three planes simultaneously
Funding provided by: Human Frontiers Science Program
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000854
Award Number: LT000759/2014
Funding provided by: Canadian Institute for Health Research*
Crossref Funder Registry ID:
Award Number: FDN143227
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: P20GM113109
Funding provided by: Human Frontiers Science Program
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000854
Award Number: RGP0016/2019
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: R35GM142566
| Name | Size | |
|---|---|---|
|
20180219_topro_average_2020.nii.gz
md5:9a5d5ec9e856a04a3f089f55f08efeac |
384.0 MB | Download |
|
20180505_calbindin_average.nii.gz
md5:cae91546e856abc6a525b1bc9bd0e740 |
164.0 MB | Download |
|
20180505_TH_average.nii.gz
md5:638f161b268ed58471d12d1280c54b28 |
189.8 MB | Download |
|
20180628_AF_average.nii.gz
md5:a8d28bbb5bce35cd1776842e0e6850ff |
293.6 MB | Download |
|
20180815_5-HT_average.nii.gz
md5:bc4312ed95ea100bd3bedb7bc231918e |
226.0 MB | Download |
|
20180815_GFAP_average.nii.gz
md5:bdbdd72efa40e60979cd7b28ae13f226 |
138.0 MB | Download |
|
20180815_HuCD_average.nii.gz
md5:680db6ab399801973916f4d0b0e65684 |
211.6 MB | Download |
|
20180815_PCNA_average.nii.gz
md5:f5b061be9a5550bb19e84dcb2c674d84 |
164.9 MB | Download |
|
20180815_Prox1_average.nii.gz
md5:ee4929fb7be2a21b62d69e90fdb27e22 |
189.2 MB | Download |
|
20181120_Calretinin_average.nii.gz
md5:345bfbce0aa8fc5c1251756c946d0ca1 |
185.0 MB | Download |
|
20181120_ChAT_average.nii.gz
md5:f38fdeebadf6bfd490c5627bc10e10b9 |
241.7 MB | Download |
|
20181120_PV_SWANT_average.nii.gz
md5:1fe127be9c431e0c74476f78ed937f2c |
240.6 MB | Download |
|
2021-08-22_AZBA_Label_descriptions.txt
md5:04b574458701df148574aed62d5cbf43 |
16.6 kB | Download |
|
2021-08-22_AZBA_segmentation.nii.gz
md5:13c816a416ff1e3db98211f4882a0983 |
3.4 MB | Download |
|
2021-08-22_AZBA_structure_tree.txt
md5:3239ef61da1c9a8efc3d033a8d2ae45f |
11.5 kB | Download |
|
ReadMe.pdf
md5:547f9c208fa9fb61602a8d6c1fd8fc15 |
146.9 kB | Download |
| Views | 91 |
| Downloads | 167 |
| Data volume | 14.4 GB |
| Unique views | 85 |
| Unique downloads | 82 |
Indexed in
- Publication date:
- November 22, 2021
- DOI:
-
- Keyword(s):
- Adult Zebrafish 3D segmented Atlas Light-sheet Imaging Tissue clearing Brain atlas Image registration AZBA Adult Zebrafish Brain Atlas Danio rerio
- Related identifiers:
- Cited by
- Communities:
- License (for files):
- Creative Commons Zero v1.0 Universal