The HUDSEN Atlas: a three-dimensional (3D) spatialframework for studying gene expression in thedeveloping human brainJanet Kerwin,1 Yiya Yang,2 Paloma Merchan,3 Subrot Sarma,1 Jessica Thompson,1 Xunxian Wang,1

Juan Sandoval,3 Luis Puelles,3 Richard Baldock2 and Susan Lindsay1

1Institute of Human Genetics, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, UK3Department of Human Anatomy and Psychobiology, and CIBER en Enfermedades Raras U736, Faculty of Medicine, University

of Murcia, Murcia, Spain

Abstract

We are developing a three-dimensional (3D) atlas of the human embryonic brain using anatomical landmarks

and gene expression data to define major subdivisions through 12 stages of development [Carnegie Stages

(CS) 12–23; approximately 26–56 days post conception (dpc)]. Virtual 3D anatomical models are generated from

intact specimens using optical projection tomography (OPT). Using MAPAINT software, selected gene expression

data, gathered using standard methods of in situ hybridization and immunohistochemistry, are mapped to a

representative 3D model for each chosen Carnegie stage. In these models, anatomical domains, defined on

the basis of morphological landmarks and comparative knowledge of expression patterns in vertebrates, are

linked to a developmental neuroanatomic ontology. Human gene expression patterns for genes with charac-

teristic expression in different vertebrates (e.g. PAX6, GAD65 and OLIG2) are being used to confirm and ⁄ or

refine the human anatomical domain boundaries. We have also developed interpolation software that digi-

tally generates a full domain from partial data. Currently, the 3D models and a preliminary set of anatomical

domains and ontology are available on the atlas pages along with gene expression data from approximately

100 genes in the HUDSEN Human Spatial Gene Expression Database (http://www.hudsen.org). The aim is that

full 3D data will be generated from expression data used to define a more detailed set of anatomical domains

linked to a more advanced anatomy ontology and all of these will be available online, contributing to the

long-term goal of the atlas, which is to help maximize the effective use and dissemination of data wherever it

is generated.

Key words 3D atlas; database; gene expression; human embryo; optical projection tomography.

Introduction

The human brain has a highly complex anatomical structure

and achieving this through development requires the coor-

dinated expression of sets of genes. These patterns are

often directed by morphogen signals diffusing from orga-

nizer regions, which specify and determine cell fate and

location. A major focus of developmental neuroscience is to

understand how this specificity is attained: the identifica-

tion of genes which control the development of key brain

regions and how the regions themselves develop spatially

in 3D and temporally during gestation and postnatal devel-

opment (morphogenesis and histogenesis). Gaining insight

into the genetic programme that regulates normal brain

development in human has further implications for the

understanding of developmental disorders resulting in neu-

rological impairment.

Much of the work on determining patterns of gene

expression in the developing brain has been carried out in

the mouse and other organisms, but less so in human. In

organisms such as mouse or zebrafish, visualization of gene

expression patterns can be achieved relatively easily at early

stages using wholemount staining techniques. Inevitably,

wholemount experiments are rarely (if ever?) possible with

material that has limited availability, such as human

embryos. Instead, 2D spatial gene expression patterns are

obtained from serially sectioned embryos using in situ

hybridization or immunohistochemistry. Some of the big-

gest challenges in the interpretation of these data in organs

Correspondence

Janet Kerwin, Institute of Human Genetics, Newcastle University,

International Centre for Life, Central Parkway, Newcastle upon Tyne,

NE1 3BZ, UK. E: j.m.kerwin@ncl.ac.uk

Accepted for publication 29 July 2010

ªª 2010 The AuthorsJournal of Anatomy ªª 2010 Anatomical Society of Great Britain and Ireland

J. Anat. (2010) 217, pp289–299 doi: 10.1111/j.1469-7580.2010.01290.x

Journal of Anatomy

such as the developing human brain are how to relate the

2D section data to what is a complex and intricate 3D ana-

tomical structure and how to compare gene expression pat-

terns from one stage of development with another within

the same species or amongst different species.

Different projects have addressed these issues in various

ways: projects working on species such as Xenopus

(Bowes et al. 2010), Caenorhabditis elegans (Harris et al.

2010) and Drosophila (Lecuyer et al. 2007) have opted for

a system whereby wholemount images are displayed with

a text-based description of the sites of expression. In

more complex organisms such as the mouse, there are

atlases such as the Allen Brain Atlas (Lein et al. 2007) and

GENSAT (Heintz, 2004) which deliver gene expression pat-

terns from serially sectioned tissue, linked to a colour-

coded reference atlas of 2D annotated sections. Another

method, used by the Edinburgh Mouse Atlas of Gene

Expression (EMAGE; Baldock et al. 2003) and the Atlas of

Zebrafish Development (Verbeek et al. 1999), has been to

create a series of 3D reference models to provide a spatial

framework in which anatomical structures are defined,

and into which 2D experimental data can be mapped.

This is the approach we have taken for the HUDSEN atlas.

Our 3D reference models are generated from intact

human embryos using the rapid and non-invasive tech-

nique of optical projection tomography (OPT; Sharpe

et al. 2002). The HUDSEN atlas is based on 12 such OPT

models covering the range of Carnegie Stages CS12

(approximately 26 dpc; the closure of the caudal neuro-

pore) to CS23 (approximately 56 dpc; the end of the

embryonic period, when all the major organs have devel-

oped). The OPT models are visualized and manipulated

using custom-designed software, MAPAINT, developed as

part of the Edinburgh Mouse Atlas Project (http://www.

emouseatlas.org).

The HUDSEN atlas and human spatial gene expression

database are delivered via the project website (http://

www.hudsen.org). The project aims to define within the 3D

models a number of subdivisions of the CNS, linked to a cor-

responding ontology based on the prosomeric model of the

vertebrate forebrain (Puelles & Rubenstein, 2003), a model

of transversal and longitudinal brain subdivisions developed

by comparing a large number of gene expression patterns

and correlated homologous anatomical landmarks across

different vertebrate species (Puelles et al. 2004, 2007; Ferran

et al. 2009; Pombal et al. 2009; Puelles – reference atlases

for the Allen Brain Atlas: Developing Mouse Brain project,

http://developingmouse.brain-map.org/; released March

2010).

Conventional in situ hybridization or immunohistochem-

ical experiments in human embryos generate series of 2D

section data with intricate gene expression patterns,

which can be difficult to conceptualize without a 3D con-

text. Planes of section can vary widely among specimens,

making interpretation even more problematic. Our OPT

models act as a 3D anatomical framework whereby data

from different experiments can be mapped into the same

space and later visualized in any section plane, greatly

facilitating the interpretation of the results. As an ongo-

ing process, 2D section data from immunohistochemistry

or in situ hybridization experiments are also mapped into

the models to generate entries in the spatial gene expres-

sion database. Data entry from other groups is encour-

aged. We will map all data to the same 3D reference

models which will enable direct comparisons of data for

multiple genes as well as for data generated by different

groups.

Methods

Embryo collection

Human embryonic and fetal tissues were obtained from the

MRC-Wellcome Trust Human Developmental Biology Resource

(http://www.hdbr.org; Lindsay & Copp, 2005), Institute of

Human Genetics, Newcastle University. The samples were col-

lected with appropriate maternal consents and ethical approval

by the Newcastle and North Tyneside Research Ethics Commit-

tee. Embryos were staged and fixed overnight in 4% parafor-

maldehyde at 4 �C before being stored in 70% ethanol prior to

OPT imaging or wax embedding and sectioning at 8 lm. Placen-

tal tissue was sampled for karyotype analysis prior to fixation of

the embryo tissue.

OPT

The 3-dimensional models were generated from intact,

unstained human embryos, using optical projection tomography

(OPT). Fixed specimens were rehydrated through a graded series

of ethanol and embedded in a block of 1% low melting point

agarose. The blocks were dehydrated and cleared, and the spec-

imens were rotated through 360�, as 400 images were captured

at 0.9� intervals. The signal corresponded to the weak autofluo-

rescence originating from the paraformaldehyde-fixed tissue,

and was detected using a wideband FITC filter with excitation

at 465–500 nm and emission at 515–560 nm. The 400 captured

images were then assembled into a voxel-volume that recreates

the 3D shape of the embryo, using modified tomography algo-

rithms (Sharpe et al. 2002).

Anatomical domain painting

The OPT models are visualized and manipulated using the cus-

tom-designed software, MAPAINT, developed as part of the Edin-

burgh Mouse Atlas Project (http://genex.hgu.mrc.ac.uk). The

software enables the user to select a digital section at any arbi-

trary angle and position through a model, and compare a

number of different planes simultaneously or in sequence.

Neuroanatomical regions were manually ‘painted’ and corrected

for accuracy using MAPAINT. For each boundary traced, the opti-

mal section plane for visualizing it was selected (usually perpen-

dicular to the boundary), and the initial painted domain was

checked and refined using orthogonal views, thus correcting its

3D shape.

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The HUDSEN electronic atlas of the developing human brain, J. Kerwin et al.290

Immunohistochemistry

Sections were mounted two to a slide, and alternate one-in-10

slide series were stained with antibodies against PAX6 (PRB-

278P, Covance), GAD65 (ab49830, Abcam) and OLIG2 (AB9610,

Millipore), using standard techniques. The reaction was visual-

ized with diamino benzidine and the sections lightly counter-

stained with toluidine blue.

Gene expression mapping

Images of the stained sections were captured through a ·1.25

objective (as viewed down the microscope at 12.5· magnifica-

tion) using the Zeiss Axiovision system. Each image was cap-

tured at 1300 · 1030 pixels, at a resolution of 8.2 lm per pixel.

After capturing high quality low-power images of the experi-

mental data, the corresponding section plane and respective

positions were identified in the OPT model by an experienced

user. Using a modified warping interface in MAPAINT, correspon-

dences between the experimental and digital images were then

identified and manually defined. The experimental image was

then transformed to the shape of the digital section, and the

image transformation saved. The interface uses interactive thres-

holding to extract the expression signal from the experimental

image, and then applies the image transformation to map this

signal into the space of the 3D OPT model. This was done for

each of the experimental images in turn, generating a gene

expression domain. We report here examples of such material.

For the CS19 OLIG2 domain, five sections were mapped through

the forebrain of the CS19 representative model, and for CS22,

PAX6, GAD65 and OLIG2 the domain consisted of approximately

20 sections for each gene through the forebrain of the CS22

representative model.

Results

In the Ongoing Work sections below we describe the pro-

gress made to date with generating the components of the

HUDSEN Atlas and Human Spatial Gene Expression Data-

base. This includes work that has been completed but is not

yet web-accessible. The Current Status sections summarize

what is already publicly available (http://www.hudsen.org).

HUDSEN atlas

Current status

There are individual pages for each stage from CS12 to

CS23 which include stage definitions and movies of a num-

ber of OPT models. Using the reference OPT model for each

stage, there is also a viewer with standard sections in the

three orthogonal planes linked to a basic ontology. The

CNS has been defined in all the 3D models. The Atlas home

page also includes links to a table giving the criteria we use

for staging human embryos and a table comparing human

and mouse developmental stages. At present the user can-

not interact fully with the 3D models over the web. How-

ever, we provide the 3D models on CD ⁄ DVD in the Java

Atlas Viewer (Feng et al. 2005), including the detailed ana-

tomical domains where these are available (currently CS17,

CS19 and CS22). A link to a request form is given on the

Atlas home page. The detailed anatomical domains are not

yet available online but will be once the WlzIIP viewer (Husz

et al. 2009 and see below) is brought into the site.

Ongoing work

Defining anatomical domains. The authors (L.P., P.M.

and J.S.) defined the boundaries and position of individual

domains in the human models on the basis of identifiable

morphological features (CS17, CS19 and CS22). Morphologi-

cal landmarks and features visible in the human models

were used to guide the painting of individual 2D digital sec-

tions. Features of the brain midline, surface and nerve roots

were particularly useful. These paintings were later incre-

mentally built up into a 3D domain whose 3D shape was

corrected by viewing all the component 2D sections in

other, usually orthogonal, planes. Figure 1 shows the subdi-

visions of the central nervous system that have been

defined so far in the CS22 model. The domains can be visu-

alized in 2D sections (Fig. 1A) or in 3D (Fig. 1B), and are

linked to the ontology shown in Fig. 1D. A movie of the

painted CS22 model is available in the Supporting Informa-

tion Movie S1.

The neural-tube developmental ontology (Puelles –

ontology developed for the Allen Developmental Brain

Atlas, http://developingmouse.brain-map.org/; release

March 2010; see also Ng et al. 2009) is a single conceptual

framework applicable for all stages of development from

early neural plate stages (level 0) through to the adult

(levels 12 ⁄ 13). It proceeds by progressive subdivision of

early parts, first anteroposterior planar regions in the neu-

roepithelium (brain vesicles and segments – levels 1–3),

then dorsoventral planar regions (alar, basal, roof and

floor plates – levels 4, 5) and finer planar subdivisions

where required (levels 6–8), and, finally, primary radial

subdivisions (ventricular and mantle layers; immature man-

tle strata – levels 9, 10) and definitive nuclei, eventually

with internal subdivisions (levels 11–13). To date, the HUD-

SEN models of human development have been painted up

to level 3 of this ontology (segments; see Fig. 1). The neu-

ral-tube developmental ontology will be brought into the

atlas and delivered using the WlzIIP server technology

(Husz et al. 2009) which allows the user to view arbitrary

sections through the embryo models in conjunction with

selectable anatomical regions.

Generating gene expression data to refine and test

the anatomical domains. Usually, anatomical domains

can be defined to a much higher resolution if gene expres-

sion data are also available (as was the case for the Allen

Brain Atlas: Developing Mouse Brain project). Given the

more limited availability of human tissue, a restricted set of

genes (Table 1) was chosen to help define the major

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The HUDSEN electronic atlas of the developing human brain, J. Kerwin et al. 291

boundaries within the developing forebrain from stages

CS19 to CS23.

Figure 2 gives examples of PAX6, GAD65 and OLIG2

expression at CS22. As can be seen from Table 1, these

genes had expression patterns that were predicted to

define pallium (PAX6; Carney et al. 2009; Puelles et al.

2000; Yun et al. 2001) and subpallium (GAD65 and OLIG2;

Tekki-Kessaris et al. 2001; Lopez-Bendito et al. 2004; Sun

et al. 2005; Mo & Zecevic, 2008) within the developing tel-

encephalon, as well as prosomeres 3 and 1 in the develop-

ing diencephalon (PAX6 and GAD65; Mastick et al. 1997;

Katarova et al. 2000; Ferran et al. 2008). Within the striatal

subpallium, PAX6 has a weak expression pattern that

allows the lateral and medial ganglionic eminences to be

distinguished (Flames et al. 2007). As can be seen from

Fig. 2, the expression patterns of the three genes match

almost precisely the defined anatomical domain boundaries

for the pallium and subpallium. The exact boundaries of

the lateral and medial ganglionic eminences, or of the pre-

optic area, cannot be distinguished by morphology alone

and so have not been painted in the models, pending fur-

ther gene marker support. Adding specific expression pat-

terns, such as that of Nkx2.1, will allow these domain

boundaries to be defined. For domains defined on the basis

of gene expression alone, multiple expression patterns will

be needed. The expression patterns defining specific

domains will be made explicit, as notes to the annotations

and the gene expression data themselves will be available

in the HUDSEN Human Gene Expression Spatial Database

(see below).

Generating full 3D expression domains by data

interpolation: As is often the case, expression data from

more than one gene are needed to characterize a given

A

C D

B

Fig. 1 Painted anatomical domains in 2D and

3D. This shows the subdivisions of the central

nervous system that have been defined in the

CS22 model. The domains can be visualized

in 2D sections (A) or in 3D (B), and are linked

to the ontology shown in (D). The colour

scheme is indicated in the key (C).

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neural tube region (e.g. the combined expression of PAX6

and PAX3 is required to define the pretectal region; Ferran

et al. 2007), which usually means that a fully informative 3D

expression domain for any single marker cannot be built up

from data from one embryo. One solution we are using is

to generate data from multiple embryos of the same stage

and map these to the representative 3D model. We have

also developed a computational method to help solve the

problem of how to use optimally sparse 2D section data to

infer the full 3D patterns of expression: the 3D INTERPOLATION

AND DOMAIN MAKER software (3D-IDM; Wang et al. 2010). 3D-

IDM consists of steps that operate at different levels to

identify the individual components of a gene expression

pattern, to cluster elements that belong together, to track

components between sections, to match the shapes of

components from section to section and to interpolate

A B C

G H

D

FE

Fig. 2 Comparison of painted domains with gene expression data. This shows data from immunohistochemical experiments at CS22. Each image

was captured at a resolution of 8.2 lm ⁄ pixel. PAX6 (A,E) has been compared with GAD65 (B) and OLIG2 (F), at 2 levels through the head of a

CS22 embryo [the section plane is indicated in the sagittal views (D,H)]. When digital sections from the painted OPT model (C,G) are aligned with

the experimental sections it becomes evident that the gene expression patterns define boundaries between different anatomical regions. Both

PAX6 (A) and GAD65 (B) are strongly expressed in the pallium (red) and define the boundary between the pallium and subpallium (orange). Both

genes are also strongly expressed in Prosomere 3 (green), stopping at the boundary with the hypothalamus [painted in brown, the boundary

indicated with a white arrow in (A) and (B)]. PAX6 is more weakly expressed within the striatal subpallium, allowing the boundary between the

medial and lateral ganglionic eminences [white arrowhead in (A)] to be distinguished. At a slightly more caudal level, PAX6 (E) has been compared

with OLIG2 (F). At this section level PAX6 is expressed strongly in both the pallium and hypothalamus, but negative in the subpallium. In both

areas the expression stops sharply at the subpallial boundary (black arrowheads). PAX6 also defines the alar ⁄ basal boundary (black arrow) within

rhombomere 1 (painted purple) in the hindbrain. In contras, OLIG2 is expressed strongly in the subpallium, but is negative in the pallium.

Table 1 A list of a restricted set of well characterized genes chosen to define boundaries within the developing forebrain from stages CS19 to

CS23.

Gene Boundary References

DBX1 Ventral pallium to pallio-subpallial border (PSB) Medina et al. (2004)

GAD65 Subpallium to PSB, prosomere 3 to hypothalamus Lopez-Bendito et al. (2004), Sun et al. (2005)

GAP43 Cranial nerves and major axonal tracts Meiri & Burdick (1991)

OLIG2 Subpallium to PSB Tekki-Kessaris et al. (2001), Mo & Zecevic (2008)

OTX2 ZLI, caudal midbrain border Simeone et al. (2002)

PAX6 Pallium to PSB, hypothalamus to subpallium, forebrain

(diencephalon; p1) to midbrain, and r1 to r2 hindbrain

boundary

Puelles et al. (2000), Matsunaga et al. (2000),

Walther & Gruss (1991)

PAX7 Hindbrain alar-basal, midbrain to rostral prosomere 1 Jostes et al. (1990)

SHH ZLI, floorplate Ericson et al. (1995), Odent et al. (1999)

TBR1 Pallium to PSB, also amygdala and prosomere 3 Puelles et al. (2000)

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expression patterns on ‘in between’ sections. A set of algo-

rithms carries out the clustering, tracking, shape matching

and interpolating automatically, and a graphical user inter-

face (GUI) is provided to guide and ⁄ or correct the results

generated by the automated algorithms in each step.

The 3D-IDM software has been used to generate a full 3D

gene expression domain for OLIG2 in the forebrain at CS19.

As described in the Methods section, immunohistochemistry

was carried out for a discontinuous series of sections

through the forebrain of a CS19 embryo, and the individual

section data were mapped to the CS19 OPT model. An

example of the experimental data is shown in Fig. 3A, with

mapped data being shown in Fig. 3E. This mapping is car-

ried out section by section to incrementally build up the 3D

expression pattern (shown in red in Fig. 3A). The original

section plane is indicated on the sagittal view (Fig. 3D).

Note that when the angle of section is changed (indicated

on the sagittal view in Fig. 3G) the domain results in a series

of lines where the section plane intersects the individual 2D

domains (Fig. 3H). As described above, the 3D-IDM software

tracks and matches components in individual sections and

interpolates the expression patterns on the intervening

sections, generating a smooth 3D domain that can be cut,

checked and refined in any plane. The interpolated 3D

domain for our example is shown in cyan in Fig. 3C, the

spaces between the sections having been ‘filled in’, and the

domain no longer appears as a series of lines on the 2D

section, but as a continuous area which can be digitally cut

in any orientation, whether it is the original section plane

(Fig. 3F), or an arbitrary one (Fig. 3I).

A

D E F

G H I

B C

Fig. 3 3D OLIG2 expression domain at CS19. A 3D gene expression pattern for OLIG2 in the forebrain of the CS19 model was generated by

mapping a series of 2D immunohistochemical sections, an example of which is shown in (A). This mapping is carried out section by section to

incrementally build up the 3D expression pattern [shown in red in (B)]. The original section plane (E,F) is indicated on the sagittal view (D). Note

that when the angle of section is changed [indicated on the sagittal view in (G)] the domain is displayed as a series of lines where the section

plane intersects the individual 2D domains (H). As described above, the 3D-IDM software tracks and matches components in individual sections

and interpolates the expression patterns on the intervening sections, generating a smooth 3D domain that can be cut, checked and refined in any

plane. The interpolated 3D domain for our example is shown in cyan in (C), the spaces between the sections having been ‘filled in’, and the

domain no longer appears as a series of lines on the 2D section, but as a continuous area (I), as in the original section plane (F).

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The HUDSEN electronic atlas of the developing human brain, J. Kerwin et al.294

HUDSEN human gene expression spatial database

Current status

The database is delivered to the user at http://www.HUD

SEN.org. Figure 4A shows the home page with a table of

the 104 genes currently contained in the database. In

general, data is collected in a way that conforms to

MISFISHIE guidelines (Deutsch et al. 2008), which lay down

a set of standards for reporting and exchanging gene

expression results, and should allow the data to be inde-

pendently evaluated and reproduced. Where there are

sufficient data to determine the plane of section (usually

a minimum of three sections from the same embryo), the

data are spatially mapped into the standard reference

models and can be visualized in 2D or 3D. Otherwise,

the data is text-annotated using the current basic ontol-

ogy. Data entry into the database by other groups is

welcomed. See Supporting Information for submission

instructions.

Data can be retrieved in three ways, by browsing the

entire contents of the database, or by searching for a spe-

cific gene name or anatomical term. A search for PAX6 is

shown in Fig. 4B. For each dataset a 3D view of the expres-

sion pattern is shown, together with a list of structures in

which the gene is expressed, and an indication of whether

the expression is strong (red), moderate (yellow) or weak

(blue). Pressing the gene name provides a link to the

Ensembl entry for that particular gene (Ensembl: http://

www.ensembl.org/index.html).

Selecting the EADHB ID brings up the database entry

(shown in Fig. 4C). Full resolution images of the original

experimental sections can be displayed by a mouse click on

the thumbnail image. Below these images is the quality rat-

ing of the data (in this case, three stars (see Supporting

A

B

C

Fig. 4 The HUDSEN gene expression database. (A) Home page of the HUDSEN database website (http://www.HUDSEN.org) displaying a table of

the genes currently contained in the database. (B) The results of a search for PAX6. The database can be queried in a number of ways: by

Anatomical name, Carnegie Stage, Gene or Probe ID. Alternatively, the entire contents of the database can be displayed for browsing. (C)

Screenshot of an entry in the HUDSEN Database showing PAX6 expression at CS22. Thumbnail images of the experimental sections and the

expression mapped onto the OPT sections can be clicked on to provide full resolution images. A 3D view showing the 3D context of the mapped

data is also provided, which can be downloaded as a movie. Where gene expression intersects with painted anatomical domains, percentage data

is shown, providing both relative quantitative and qualitative information about the sites of the gene expression. In addition, probe ⁄ antibody

information is provided, together with any related publications.

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The HUDSEN electronic atlas of the developing human brain, J. Kerwin et al. 295

Information Data S1 for Editorial Policy and guide to creat-

ing database entries). Details of the detection reagent (anti-

body supplier or accession number and nucleotide

sequence of probes) are given in the next panel. The gene

expression is described in a number of ways: where the sites

of expression have been manually annotated, a table of

structures is generated showing the level of intensity

(strong, moderate, weak, possible expression or not

detected). For patterns that have been spatially mapped,

images of the individual 2D OPT sections are displayed with

an image of the 3D context of the mapped data, which can

be downloaded as a movie. As each reference model is

linked to the ontology, where gene expression intersects

painted anatomical domains, percentage data are shown,

providing both relative quantitative and qualitative infor-

mation about the sites where gene signal is present. In

addition, any relevant publications are provided, together

with links to the same gene in other databases [The Edin-

burgh Mouse Atlas of Gene Expression (EMAGE) http://

www.emouseatlas.org/emage/, BioGPS; http://biogps.gnf.

org and Allen Brain Atlas; http://www.brain-map.org/].

Once a gene expression pattern has been chosen, it is

possible to search for gene expression patterns that are spa-

tially similar to that entry by pressing the ‘find similar’ icon.

This creates a list of entries showing the genes that have

been spatially mapped to the same structures in the same

representative model.

Ongoing work

There is an ongoing effort to add gene expression data,

generated both in-house and from other groups (either

submitted directly or via their publications). Data sets for

the genes in Table 1 are being generated for stages

CS19–CS23 with additional data for five of the nine genes

being generated for stages CS14–CS18. All these data sets

will be uploaded to the database along with notes indi-

cating the boundaries and ⁄ or regions that they have

been used to define. These notes will link to the same

domains in the corresponding reference model in the

Atlas. As is the case for all the entries, the original section

images as well as the thresholded and mapped data will

be present, so that database users will be able to judge

both the data and their interpretations for themselves.

The Puelles neural tube developmental ontology will also

be brought into the database and used for text-based

mapping of data. This will enable more detailed text-

based querying of the database. Similarly, as more

domains are defined and painted on the reference mod-

els they will be used for spatial mapping of the expres-

sion data. Again, this will mean more detailed spatial

queries are possible.

Relationships from one developmental stage to another

will also be made via the developmental ontology and

linked painted domains. Eventually, 4D analysis of gene

expression patterns will be possible, for example by identi-

fying data entries for the same ontology entity across all

stages included in HUDSEN.

Future plans

The main goal is to integrate the atlas and gene expression

database more closely and to enable the user to view and

manipulate data interactively in 3D. The user, for example,

would be able simultaneously to view one or more gene

expression patterns and all of the painted anatomical

domains within the same 3D OPT model. The Wlz IIP viewer

already allows the 3D models to be viewed and manipu-

lated interactively over the web and a prototype portal has

been designed that holds anatomical domains as well as

other types of educational material (for information see

The HUDSEN Electronic atlas of the developing human

brain and human spatial gene expression database http://

www.hudsen.org/next-generation-embryology/). There are

significant technical and conceptual challenges to deliver-

ing 3D gene expression data while preserving the structure

and metadata within the gene expression database. We will

start by generating and delivering 3D expression domains

for the marker genes in Table 1.

Discussion

In the HUDSEN Atlas, anatomical domains are structured

within the single conceptual framework of the neural-tube

developmental ontology, developed by one of the authors

(L.P.) for the Allen Developmental Brain Atlas. For a spatial

atlas, such as the HUDSEN atlas, the key mechanism for link-

ing spatial and anatomical information is to define the ana-

tomical domains (by ‘painting’ them) within the 3D

representative models.

The authors (L.P., P.M. and J.S.) defined the boundaries

and position of individual domains in the human models on

the basis of identifiable morphological features and land-

marks that were visible in the human models (e.g. anatomic

accidents of the midline of the brain; ventricular relief;

nerve roots; commissures and decussations; other character-

istic fibre tracts; choroidal or glandular specializations; char-

acteristic bulges and constrictions of the neural tube wall).

Useful images for comparison were found in classic human

neuroembryology atlases, e.g. Hochstetter (1919, 1923,

1929) and Lemire et al. (1975), plus the recent developmen-

tal human brain atlases of O’Rahilly & Muller (2005) and

Bayer & Altman (2005, 2006, 2008), even though different

interpretive models were used and discrepancies exist on

various specific points.

Gene expression data can be used to confirm and refine

the painted domains. However, we took the decision that

modifications to painted domains should be made on the

basis of reproducible discrepancies between the expression

patterns for at least two genes and the painted domain. To

date, we have only defined domains at the first anteropos-

terior planar regions in the neuroepithelium (brain vesicles

ªª 2010 The AuthorsJournal of Anatomy ªª 2010 Anatomical Society of Great Britain and Ireland

The HUDSEN electronic atlas of the developing human brain, J. Kerwin et al.296

and segments: levels 1–3; see http://developingmouse.brain-

map.org/; released March 2010 and Ng et al. 2009) at CS17,

CS19 and CS22. For each of these stages only those domains

for which there is sufficient morphological information

within the corresponding 3D OPT models have been

defined. For example, the extent of prosomere 1 in the alar

plate is given by the posterior commissure, while in the

basal plate it is approximated by the oculomotor nerve root

caudally and the fasciculus retroflexus (habenulo-interpe-

duncular tract) rostrally (Verney et al. 2001).

The genes chosen to confirm these domains (Table 1)

are well-characterized and show consistent expression pat-

terns across several vertebrate species so it is perhaps not

surprising that their expression patterns match closely the

relevant painted domains. Further subdivisions may have

to rely more heavily on gene expression data and for these

it will be important to define domains based on the

expression patterns of at least two, and ideally more,

genes. Also, genes are often expressed more widely ini-

tially and it is as their pattern becomes restricted after

closure of the neural tube that they progressively define

boundaries between anatomical regions. This will limit the

number of subdivisions that can be painted at earlier

developmental stages. It will also be important that all the

gene expression data are available for other researchers to

review independently.

Using the OPT models as a standard framework enables

gene expression patterns to be compared within the same

3D space for each developmental stage in the atlas and

database (CS12–CS23). This has the advantage that results

from different experiments or even different research

groups can be directly compared. Warping expression data

for the same gene from multiple samples into the same 3D

space will enable the consistent aspects of its expression pat-

tern to be reproducibly defined. Small differences between

experiments and ⁄ or samples are likely to be lost as data are

warped to a representative space, which will help to over-

come the problem of biological variation. Furthermore,

mapping the data to representative 3D models allows the

data to be processed by automatic methods, e.g. for pattern

recognition, or cluster analysis (Venkataraman et al. 2008).

The atlas and gene expression database are linked

through the anatomical ontology and defined painted

domains in the same set of reference models. Accurate

annotation and sufficient sampling of the gene expression

patterns is important both for the effective searching and

retrieval of information from the database, and for the ease

of interpretation of the results, particularly for non-expert

users. Anatomical annotation is done in two ways. First,

manual text annotation which allows the database to be

queried by text-based searches and is advantageous for

those structures which have not yet been painted, or to

describe gene expression in subdivisions of a structure that

are not morphologically visible in the OPT models. Sec-

ondly, where a gene expression pattern overlaps a painted

anatomical domain, the annotation is automatically gener-

ated according to the ontology. This automatic method of

generating annotation has the benefit that in future the

painted domains could be linked to one or more ontolo-

gies. This is an option which would be valuable for struc-

tures where the boundaries are poorly defined or disputed.

The user could check alternative morphologic interpreta-

tions, or simply visualize correspondences between variously

complex ontologies. The consistency of expression patterns

observed across many vertebrate species suggests that there

is a fundamental conservation of the genomic control of

early patterning and histogenetic brain development across

all vertebrates. As evidence accumulates, this may mean

that our developmental neuroanatomic ontology will not

only serve for comparing human and rodent brains

(HUDSEN and Allen Mouse Atlases), but actually represent a

conceptual framework able to inter-relate all sorts of com-

parative neuroanatomic data (other mammals, sauropsids,

amphibia, fishes).

A recent review of developmental gene expression atlases

(de Boer et al. 2009) concluded that an ‘ideal’ atlas should

be based on a series of 3D reference models, anatomically

annotated using a high resolution ontology. The HUDSEN

Atlas aims to attain this ideal: although not yet fully anno-

tated to a high resolution, it does provide a unique 3D spa-

tial anatomical framework associated to a flexible

developmental ontology for studying and understanding

gene expression in early human prenatal development.

Acknowledgements

The project is funded by the US National Institutes of Health

(grant: 5RO1MH070370), EU FP6 Research Infrastructure Action

‘Structuring the European Research Area’ Programme (Contract

number 011993), the Spanish Ministry of Science and Innovation

grant BFU2008-04156 and SENECA Foundation contract

04548 ⁄ GERM ⁄ 06-10891. The human tissue was provided by the

Joint MRC-Wellcome Human Developmental Biology Resource

(http://www.hdbr.org) IHG, Newcastle upon Tyne.

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Supporting Information

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Movie S1. A movie of the painted CS22 model. For the colour-

code, please refer to legend to Fig. 1C.

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