Table 1.

Summary of anatomical atlases surveyed

Atlas	Description	Spatial scope	Developmental stages	URL, full project name, project leadership	Publication
C. elegans
WormAtlas	A collection of resources including the SlidableWorm (for viewing annotated electron micrograph sections) and descriptions of individual neurons.	body	adult hermaphrodite, adult male, dauer larva	http://wormatlas.org From the laboratory of David Hall at Albert Einstein College of Medicine (Bronx, NY, USA).	[45]
OpenWorm Browser (Virtual Worm)	A 3D virtual reconstruction consisting of surface models of 680 cells.	body	adult only	http://browser.openworm.org A collaboration between WormBase and OpenWorm.	[46]
Ciona intestinalis
ANISEED (“Anatomy” section)	Illustrations of ascidian embryos at selected stages, annotated with cell names.	body	egg through adult	http://www.aniseed.cnrs.fr Ascidian Network for In Situ and Embryological Data A collaboration among ascidian researchers led by Patrick Lemaire at the CRM (Montpellier, France).	[47] [48]
FABA	Confocal micrographs for standardizing developmental stages.	body	zygote through hatched larva	http://tunicate-portal.org/faba/1.4/top.html Four-dimensional Ascidian Body Atlas From the laboratory of Kohji Hotta at Keio University (Yokohama, Japan).	[49]
Drosophila
Flygut	Description of the Drosophila midgut based on anatomy, histology, and expression patterns of reporter transgenes.	midgut	adult only	http://flygut.epfl.ch This atlas complements a publication from Bruno Lemaitre’s group at EPFL (Lausanne, Switzerland).	[50]
Virtual Fly Brain	Virtual sections from a reference brain, with anatomical regions delineated.	brain	adult only	http://www.virtualflybrain.org Members of the Virtual Fly Brain team are from the University of Edinburgh (Edinburgh, Scotland) and the University of Cambridge (Cambridge, England).	[51]
Medaka
Medaka Blood Vessel Atlas	Annotated illustrations of the vasculature of embryos.	vasculature	mid-embryonic stages	http://www.shigen.nig.ac.jp/medaka/medaka_atlas Work by Misato Fujita and Sumio Isogai. Hosted online by the National BioResource Project Medaka (Japan).	[52] [53]
Mouse
Allen Developing Mouse Brain Reference Atlas	Histological sections of brain with anatomical regions delineated.	brain	four embryonic stages, four post-natal stages	http://developingmouse.brain-map.org/static/atlas Produced by the Allen Institute for Brain Sciences (Seattle, WA, USA).	[54] [55]
e-Mouse Atlas	3D reconstructions of embryos (some with anatomical regions delineated), histological sections, and a guide to embryological stages.	body	all embryonic stages, three post-natal stages	http://www.emouseatlas.org/emap/ema/home.html also known as the Edinburgh Mouse Atlas Project led by Duncan Davidson and Richard Baldock within the Medical Research Council Human Genetics Unit and the University of Edinburgh (Edinburgh, Scotland).	[56] [57] [58] [59] [60] [61] [3]
Zebrafish
FishFace	Graphics of fluorescently-labeled chondrocytes, osteoblasts, and bone matrix in the first two pharyngeal arches.	craniofacial skeleton	pharyngula through adult	https://www.facebase.org/fishface/home Created by the laboratory of Charles Kimmel at the University of Oregon (Eugene, OR, USA) as part of the FaceBase Consortium (USA).	[62]
FishNet	Virtual sections from optical projection tomography (OPT) scans (with selected sections annotated).	body	pharyngula through adult	http://www.fishnet.org.au Produced by Robert Bryson-Richardson and Peter Currie at Monash University (Clayton, VIC, Australia).	[63]
Interactive Atlas of Zebrafish Vascular Anatomy	Fluorescent angiograms as movies and annotated diagrams.	vasculature	pharyngula through larva	http://zfish.nichd.nih.gov/Intro%20Page/intro1.html Produced by Brant Weinstein’s group at the National Institutes of Health (Bethesda, MD, USA).	[64]
ZFAP	Graphics from the FishNet atlas within a viewer that shows three orthogonal planes.	body	pharyngula through adult	http://zebrafish.anatomyportal.org Zebrafish Anatomy Portal From Robert Bryson-Richardson’s group at Monash University (Clayton, VIC, Australia).	[65]
Zebrafish Atlas	Histological sections and a virtual slide viewer. Slides from two developmental stages are annotated.	body	larva through adult	http://bio-atlas.psu.edu/zf From the laboratory of Keith Cheng at Penn State College of Medicine (Hershey, PA, USA).	[66]