|
|
Zebrafish
Anatomy Project |
|
The goal of this project is to create a web-based 3D anatomy atlas in support of zebrafish investigators addressing multiple missions across the National Institutes of Health. This atlas will consist of a comprehensive set of integrated high-resolution digital images of histological sections and 3D reconstructions of anatomical structures across development and life span. These images will provide a necessary anatomical and histological spatial context within which functional genomics and gene expression studies can be placed.
Anatomical Nomenclature
If you are looking for the name of an anatomical structure in the zebrafish, the Zebrafish Model Organism Database (ZFIN) contains an anatomy database (ontology). You can browse the ontology here, or you can see a complete alphabetized list of structures here.
The complete ontology can be downloaded either here or here. However, you will need an editor such as DAG-Edit to view these files in their appropriate format.
If you have questions about zebrafish anatomy, you can direct them to us or to the curators of the ontology. If you have questions, comments, or suggestions about the ontology, you can direct them to the curators.
Serial Section Progress
|
Period |
Stage |
Age |
Serial
Sections |
Scanned |
||
|
hpf |
days |
months |
||||
|
Gastrula
|
Sheild
|
6
|
|
|
|
|
|
75% Epiboly
|
8
|
|
|
|
|
|
|
90% Epiboloy
|
9
|
|
|
|
|
|
|
Bud
|
10
|
|
|
|
|
|
|
Segmentation
|
1 Somite
|
10.3
|
|
|
|
|
|
14 Somite
|
11.6
|
|
|
|
|
|
|
20 Somite
|
19
|
|
|
|
|
|
|
26 Somite
|
22
|
|
|
|
|
|
|
Pharyngula
|
Prim-5
|
24
|
1
|
|
done
|
done
|
|
Prim 15
|
30
|
|
|
|
|
|
|
Prim 25
|
36
|
|
|
|
|
|
|
High-pec
|
42
|
|
|
|
|
|
|
Long-Pec
|
48
|
2
|
|
done
|
done
|
|
|
Pec-fin
|
60
|
|
|
|
|
|
|
Larva
|
Protruding mouth
|
72
|
3
|
|
done
|
done
|
|
|
96
|
4
|
|
done
|
done
|
|
|
|
120
|
5
|
|
done
|
done
|
|
|
|
144
|
6
|
|
|
|
|
|
|
168
|
7
|
|
|
|
|
|
Juvenile
|
|
|
30
|
1
|
|
|
|
|
|
45
|
|
|
|
|
|
Adult
|
|
|
|
3
|
|
|
|
|
|
|
12
|
|
|
|
3D Reconstructions
Each of the links below should open a Quicktime or
Quicktime-VR object. For Quicktime-VR objects, if you click on the rotating
reconstruction that opens, it should stop rotating. If you then click-and-hold
on the reconstruction, you should be able to rotate the reconstruction manually
by moving the mouse.
4 Day Fish (QuickTime) This 1 minute movie shows many of the structures that we have reconstructed from a serial sectioned 4 day zebrafish larvae.
Head Bones (QuickTime-VR) The light blue structures represent the cartilaginous structures that will become some of the bones of the head. These include the ethmoid plate, the trabeculae, and the parachordal bones. The white structures represent the cartilaginous structures that will become the ceratohyal, certobranchial, hypobranchial, and basibranchial bones. The red structures represent the cartilaginous structures that will become bones of the lower jaw. These include the mechel's-palatoquadrate bones. In this particular view, the hyosymplectic bone is light blue although it contributes to the lower jaw.
Inner Ear (QuickTime-VR) This movie presents a 3D reconstruction of the inner ear of a 7 day zebrafish larva. The cristae for the semicircular canals are green, the sensory epithelia of the utricle and saccule are blue and the otoliths are red. The light gray outlines indicate areas where a complete portion of a semicricular canal has formed.
Larva (QuickTime) In this movie of a 7 day zebrafish larva, the eyes are blue, the inner ears are green, the nervous system is yellow, the notochord is red, the swim bladder is purple, and the bones are white.
Robert Wood Johnson Medical School does not accept any responsibility for the content of this document.
Last updated: 18 July, 2007