CCF 3D Reference Object Library

Overview

The CCF 3D Reference Object Library provides anatomically correct reference organs. The organs are developed by a specialist in 3D medical illustration and approved by organ experts.

Initially, reference objects are created using data from the Visible Human male and female datasets provided by the National Library of Medicine. The male dataset comprises 1,871 cross-sections at 1mm intervals for both CT and anatomical images at a resolution of 4,096 pixels by 2,700 pixels. The female data set has the same characteristics as the Visible Human Male but axial anatomical images were obtained at 0.33 mm intervals resulting in 5,189 cross-section anatomical images. The male was white, 180.3 cm (71 inch) tall, 199-pound and was 38 years old. The female was white, 171.2 cm (67.4 inch) tall, obese, and 59 years old.

On March 12, 2021, a total of 11 reference organs became available in GLB format. Each organ can be viewed and explored using free web browsers such as Babylon.js. Screenshots and major properties of the nested reference organ objects are given in the table below.

For selected organs, 3D extraction site objects are provided. Some extraction sites resemble geometric objects (e.g., cuboids for heart) while others take the shape of one or more whole or partial anatomical structures (e.g., in spleen). The 3D extraction sites do not restrict registration to specific regions, instead they provide “expert defined landmarks” to help guide tissue registration. The extraction site objects are also used for automatic semantic annotation of tissue samples via collision detection during registration.

Standard Operating Procedures (SOP)

Terms of Use

HuBMAP data are supplied with no warranties, expressed or implied, including without limitation, any warranty of merchantability or fitness for a particular purpose or non-infringement. No warranty with respect to the HuBMAP infrastructure is provided, including without limitation, any uptime warranty. The Parties make no representations that the use of the data will not infringe any patent or proprietary rights of third parties.

License

All CCF 3D reference objects are released under Attribution 4.0 International (CC BY 4.0).

Citation

If you use the data files, please cite this effort as follows:

Browne, K., Cross, L. E., Herr II, B. W., Record, L, Quardokus, E, Bueckle, A., Börner, K. (2021). HuBMAP CCF 3D Reference Object Library. https://hubmapconsortium.github.io/ccf/pages/ccf-3d-reference-library.html. Accessed on March 12, 2021.

Reference Organs

Download organs in GLB and FBX format.

Download extraction sites for female in GLB and FBX format.
Download extraction sites for male in GLB and FBX format.

Download ASCT+B_3D-Reference-Organ-Crosswalk in CSV format.

Male: Pelvis Details
3D Model: Pelvis, Male
Anatomical Structure ID Count
# Anatomical Structures 18
bony pelvisUBERON:00012701
coccyxUBERON:00013501
iliumUBERON:00012731
ilium compact bone2
ilium spongy bone2
ischiumUBERON:00012741
ischium compact bone2
ischium spongy bone2
pubisUBERON:00012751
pubis compact bone2
pubis spongy bone2
sacrumUBERON:00036901
Female: Pelvis Details
3D Model: Pelvis, Female
Anatomical Structure ID Count
# Anatomical Structures 18
bony pelvisUBERON:00012701
coccyxUBERON:00013501
iliumUBERON:00012731
ilium compact bone2
ilium spongy bone2
ischiumUBERON:00012741
ischium compact bone2
ischium spongy bone2
pubisUBERON:00012751
pubis compact bone2
pubis spongy bone2
sacrumUBERON:00036901
Male: Brain
3D Model: Brain, Male
Anatomical Structure ID Count
# Anatomical Structures 284
brainUBERON:00009551
amygdalohippocampal area L1
amygdalohippocampal area R1
amygdaloid complex L1
amygdaloid complex R1
angular gyrus L1
angular gyrus R1
anterior amygdaloid area L1
anterior amygdaloid area R1
anterior commissure L1
anterior commissure R1
anterior cortical nucleus L1
anterior cortical nucleus R1
anterior horn of lateral ventricle L1
anterior horn of lateral ventricle R1
anterior intermediate orbital gyrus L1
anterior intermediate orbital gyrus R1
anterior nuclear complex of thalamus L1
anterior nuclear complex of thalamus R1
anterior olfactory nucleus LUBERON:00022661
anterior olfactory nucleus R1
anterior parahippocampal gyrus L1
anterior parahippocampal gyrus R1
atrium of lateral ventricle L1
atrium of lateral ventricle R1
basal forebrain L1
basal forebrain R1
basilar part of pons L1
basilar part of pons R1
basolateral nucleus basal nucleus L1
basolateral nucleus basal nucleus R1
basomedial nucleus accessory basal nucleus L1
basomedial nucleus accessory basal nucleus R1
bed nucleus of stria terminalis L1
bed nucleus of stria terminalis R1
body of caudate L1
body of caudate R1
body of hippocampus L1
body of hippocampus R1
body of lateral ventricle L1
body of lateral ventricle R1
central canal of medulla oblongata L1
central canal of medulla oblongata R1
central nuclear group L1
central nuclear group R1
centromedian nucleus of thalamus L1
centromedian nucleus of thalamus R1
cerebellar deep nuclei L1
cerebellar deep nuclei R1
cerebellar vermis L1
cerebellar vermis R1
cerebral aqueduct L1
cerebral aqueduct R1
cerebral peduncle crus cerebri L1
cerebral peduncle crus cerebri R1
cingulate gyrus caudal posterior part L1
cingulate gyrus caudal posterior part R1
cingulate gyrus rostral anterior part L1
cingulate gyrus rostral anterior part R1
claustrum L1
claustrum R1
corpus callosum L1
corpus callosum R1
cuneus L1
cuneus R1
dorsal lateral geniculate nucleus L1
dorsal lateral geniculate nucleus R1
external segment of globus pallidus L1
external segment of globus pallidus R1
fornix L1
fornix R1
fourth ventricle L1
fourth ventricle R1
frontal agranular insular cortex area Fl L1
frontal agranular insular cortex area Fl R1
frontal operculum L1
frontal operculum R1
frontal pole L1
frontal pole R1
frontomarginal gyrus L1
frontomarginal gyrus R1
gyrus ambiens L1
gyrus ambiens R1
gyrus rectus straight gyrus L1
gyrus rectus straight gyrus R1
habenular nuclei L1
habenular nuclei R1
head of caudate L1
head of caudate R1
head of hippocampus L1
head of hippocampus R1
hemisphere L1
hemisphere R1
hypothalamus LUBERON:00018981
hypothalamus RUBERON:00018981
inferior cerebellar peduncle L1
inferior cerebellar peduncle R1
inferior colliculus L1
inferior colliculus R1
inferior frontal gyrus opercular part L1
inferior frontal gyrus opercular part R1
inferior frontal gyrus triangular part L1
inferior frontal gyrus triangular part R1
inferior horn of lateral ventricle L1
inferior horn of lateral ventricle R1
inferior occipital gyrus L1
inferior occipital gyrus R1
inferior olive L1
inferior olive R1
inferior temporal gyrus L1
inferior temporal gyrus R1
ingulo parahippocampal isthmus L1
ingulo parahippocampal isthmus R1
internal segment of globus pallidus L1
internal segment of globus pallidus R1
lateral dorsal nucleus of thalamus L1
lateral dorsal nucleus of thalamus R1
lateral hemisphere of cerebellum L1
lateral hemisphere of cerebellum R1
lateral nucleus L1
lateral nucleus R1
lateral occipitotemporal fusiform gyrus occipital part L1
lateral occipitotemporal fusiform gyrus occipital part R1
lateral olfactory gyrus L1
lateral olfactory gyrus R1
lateral orbital gyrus L1
lateral orbital gyrus R1
lateral posterior nucleus of thalamus L1
lateral posterior nucleus of thalamus R1
limen insula L1
limen insula R1
lingual gyrus medial occipitotemporal gyrus L1
lingual gyrus medial occipitotemporal gyrus R1
long insular gyri L1
long insular gyri R1
mammillary region of HTH L1
mammillary region of HTH R1
mammillothalamic tract L1
mammillothalamic tract R1
medial geniculate nuclei L1
medial geniculate nuclei R1
medial nucleus L1
medial nucleus R1
medial orbital gyrus L1
medial orbital gyrus R1
mediodorsal nucleus of thalamus L1
mediodorsal nucleus of thalamus R1
midbrain tegmentum L1
midbrain tegmentum R1
middle cerebellar peduncle L1
middle cerebellar peduncle R1
middle frontal gyrus L1
middle frontal gyrus R1
middle temporal gyrus L1
middle temporal gyrus R1
midline nuclear complex L1
midline nuclear complex R1
nucleus accumbens L1
nucleus accumbens R1
occipital pole L1
occipital pole R1
occipitotemporal fusiform gyrus temporal part L1
occipitotemporal fusiform gyrus temporal part R1
olfactory bulb LUBERON:00022641
olfactory bulb R1
olfactory tract L1
olfactory tract R1
optic ratiation L1
optic ratiation R1
optic tract L1
optic tract R1
paracentral lobule caudal part L1
paracentral lobule caudal part R1
paracentral lobule rostral part L1
paracentral lobule rostral part R1
paracingulate gyrus L1
paracingulate gyrus R1
parafascicular nucleus of thalamus L1
parafascicular nucleus of thalamus R1
paravermis of cerebellum L1
paravermis of cerebellum R1
parietal operculum L1
parietal operculum R1
perirhinal gyrus rostral part of FuGt L1
perirhinal gyrus rostral part of FuGt R1
pineal body L1
pineal body R1
piriform region LUBERON:00047251
piriform region R1
planum polare L1
planum polare R1
planum temporale L1
planum temporale R1
pontine tegmentum L1
pontine tegmentum R1
postcentral gyrus L1
postcentral gyrus R1
posterior cortical nucleus L1
posterior cortical nucleus R1
posterior horn of lateral ventricle L1
posterior horn of lateral ventricle R1
posterior intermediate orbital gyrus L1
posterior intermediate orbital gyrus R1
posterior parahippocampal gyrus L1
posterior parahippocampal gyrus R1
posteroventral putamen L1
posteroventral putamen R1
precentral gyrus L1
precentral gyrus R1
precuneus L1
precuneus R1
preoptic region of HTH L1
preoptic region of HTH R1
pretectal region L1
pretectal region R1
pulvinar of thalamus L1
pulvinar of thalamus R1
putamen L1
putamen R1
pyramidal part of medulla oblongata L1
pyramidal part of medulla oblongata R1
red nucleus L1
red nucleus R1
reuniens nucleus medioventral nucleus of thalamus L1
reuniens nucleus medioventral nucleus of thalamus R1
rostral gyrus L1
rostral gyrus R1
septal nuclei L1
septal nuclei R1
short insular gyri L1
short insular gyri R1
subcallosal gyrus parolfactory gyrus L1
subcallosal gyrus parolfactory gyrus R1
substantia nigra L1
substantia nigra R1
subthalamic nucleus L1
subthalamic nucleus R1
superior cerebellar peduncle brachium conjunctivum L1
superior cerebellar peduncle brachium conjunctivum R1
superior colliculus L1
superior colliculus R1
superior frontal gyrus L1
superior frontal gyrus R1
superior occipital gyrus L1
superior occipital gyrus R1
superior temporal gyrus L1
superior temporal gyrus R1
supramarginal gyrus L1
supramarginal gyrus R1
supraoptic region of HTH L1
supraoptic region of HTH R1
supraparietal lobule L1
supraparietal lobule R1
tail of caudate L1
tail of caudate R1
tail of hippocampus L1
tail of hippocampus R1
tegmentum of medulla oblongata L1
tegmentum of medulla oblongata R1
temporal agranular insular cortex area Tl L1
temporal agranular insular cortex area Tl R1
temporal pole L1
temporal pole R1
thalamus L1
thalamus R1
third ventricle L1
third ventricle R1
transverse temporal gyrus Heschls gyrus L1
transverse temporal gyrus Heschls gyrus R1
tuberal region of HTH L1
tuberal region of HTH R1
ventral anterior nucleus of thalamus L1
ventral anterior nucleus of thalamus R1
ventral lateral nucleus of thalamus L1
ventral lateral nucleus of thalamus R1
ventral posterior lateral nucleus L1
ventral posterior lateral nucleus R1
ventral posterior medial nucleus L1
ventral posterior medial nucleus R1
white matter of forebrain L1
white matter of forebrain R1
white matter of hindbrain L1
white matter of hindbrain R1
zona incerta L1
zona incerta R1
Female: Brain
3D Model: Brain, Female
Anatomical Structure ID Count
# Anatomical Structures 284
brainUBERON:00009551
amygdalohippocampal area L1
amygdalohippocampal area R1
amygdaloid complex L1
amygdaloid complex R1
angular gyrus L1
angular gyrus R1
anterior amygdaloid area L1
anterior amygdaloid area R1
anterior commissure L1
anterior commissure R1
anterior cortical nucleus L1
anterior cortical nucleus R1
anterior horn of lateral ventricle L1
anterior horn of lateral ventricle R1
anterior intermediate orbital gyrus L1
anterior intermediate orbital gyrus R1
anterior nuclear complex of thalamus L1
anterior nuclear complex of thalamus R1
anterior olfactory nucleus LUBERON:00022661
anterior olfactory nucleus R1
anterior parahippocampal gyrus L1
anterior parahippocampal gyrus R1
atrium of lateral ventricle L1
atrium of lateral ventricle R1
basal forebrain L1
basal forebrain R1
basilar part of pons L1
basilar part of pons R1
basolateral nucleus basal nucleus L1
basolateral nucleus basal nucleus R1
basomedial nucleus accessory basal nucleus L1
basomedial nucleus accessory basal nucleus R1
bed nucleus of stria terminalis L1
bed nucleus of stria terminalis R1
body of caudate L1
body of caudate R1
body of hippocampus L1
body of hippocampus R1
body of lateral ventricle L1
body of lateral ventricle R1
central canal of medulla oblongata L1
central canal of medulla oblongata R1
central nuclear group L1
central nuclear group R1
centromedian nucleus of thalamus L1
centromedian nucleus of thalamus R1
cerebellar deep nuclei L1
cerebellar deep nuclei R1
cerebellar vermis L1
cerebellar vermis R1
cerebral aqueduct L1
cerebral aqueduct R1
cerebral peduncle crus cerebri L1
cerebral peduncle crus cerebri R1
cingulate gyrus caudal posterior part L1
cingulate gyrus caudal posterior part R1
cingulate gyrus rostral anterior part L1
cingulate gyrus rostral anterior part R1
claustrum L1
claustrum R1
corpus callosum L1
corpus callosum R1
cuneus L1
cuneus R1
dorsal lateral geniculate nucleus L1
dorsal lateral geniculate nucleus R1
external segment of globus pallidus L1
external segment of globus pallidus R1
fornix L1
fornix R1
fourth ventricle L1
fourth ventricle R1
frontal agranular insular cortex area Fl L1
frontal agranular insular cortex area Fl R1
frontal operculum L1
frontal operculum R1
frontal pole L1
frontal pole R1
frontomarginal gyrus L1
frontomarginal gyrus R1
gyrus ambiens L1
gyrus ambiens R1
gyrus rectus straight gyrus L1
gyrus rectus straight gyrus R1
habenular nuclei L1
habenular nuclei R1
head of caudate L1
head of caudate R1
head of hippocampus L1
head of hippocampus R1
hemisphere L1
hemisphere R1
hypothalamus LUBERON:00018981
hypothalamus RUBERON:00018981
inferior cerebellar peduncle L1
inferior cerebellar peduncle R1
inferior colliculus L1
inferior colliculus R1
inferior frontal gyrus opercular part L1
inferior frontal gyrus opercular part R1
inferior frontal gyrus triangular part L1
inferior frontal gyrus triangular part R1
inferior horn of lateral ventricle L1
inferior horn of lateral ventricle R1
inferior occipital gyrus L1
inferior occipital gyrus R1
inferior olive L1
inferior olive R1
inferior temporal gyrus L1
inferior temporal gyrus R1
ingulo parahippocampal isthmus L1
ingulo parahippocampal isthmus R1
internal segment of globus pallidus L1
internal segment of globus pallidus R1
lateral dorsal nucleus of thalamus L1
lateral dorsal nucleus of thalamus R1
lateral hemisphere of cerebellum L1
lateral hemisphere of cerebellum R1
lateral nucleus L1
lateral nucleus R1
lateral occipitotemporal fusiform gyrus occipital part L1
lateral occipitotemporal fusiform gyrus occipital part R1
lateral olfactory gyrus L1
lateral olfactory gyrus R1
lateral orbital gyrus L1
lateral orbital gyrus R1
lateral posterior nucleus of thalamus L1
lateral posterior nucleus of thalamus R1
limen insula L1
limen insula R1
lingual gyrus medial occipitotemporal gyrus L1
lingual gyrus medial occipitotemporal gyrus R1
long insular gyri L1
long insular gyri R1
mammillary region of HTH L1
mammillary region of HTH R1
mammillothalamic tract L1
mammillothalamic tract R1
medial geniculate nuclei L1
medial geniculate nuclei R1
medial nucleus L1
medial nucleus R1
medial orbital gyrus L1
medial orbital gyrus R1
mediodorsal nucleus of thalamus L1
mediodorsal nucleus of thalamus R1
midbrain tegmentum L1
midbrain tegmentum R1
middle cerebellar peduncle L1
middle cerebellar peduncle R1
middle frontal gyrus L1
middle frontal gyrus R1
middle temporal gyrus L1
middle temporal gyrus R1
midline nuclear complex L1
midline nuclear complex R1
nucleus accumbens L1
nucleus accumbens R1
occipital pole L1
occipital pole R1
occipitotemporal fusiform gyrus temporal part L1
occipitotemporal fusiform gyrus temporal part R1
olfactory bulb LUBERON:00022641
olfactory bulb R1
olfactory tract L1
olfactory tract R1
optic ratiation L1
optic ratiation R1
optic tract L1
optic tract R1
paracentral lobule caudal part L1
paracentral lobule caudal part R1
paracentral lobule rostral part L1
paracentral lobule rostral part R1
paracingulate gyrus L1
paracingulate gyrus R1
parafascicular nucleus of thalamus L1
parafascicular nucleus of thalamus R1
paravermis of cerebellum L1
paravermis of cerebellum R1
parietal operculum L1
parietal operculum R1
perirhinal gyrus rostral part of FuGt L1
perirhinal gyrus rostral part of FuGt R1
pineal body L1
pineal body R1
piriform region LUBERON:00047251
piriform region R1
planum polare L1
planum polare R1
planum temporale L1
planum temporale R1
pontine tegmentum L1
pontine tegmentum R1
postcentral gyrus L1
postcentral gyrus R1
posterior cortical nucleus L1
posterior cortical nucleus R1
posterior horn of lateral ventricle L1
posterior horn of lateral ventricle R1
posterior intermediate orbital gyrus L1
posterior intermediate orbital gyrus R1
posterior parahippocampal gyrus L1
posterior parahippocampal gyrus R1
posteroventral putamen L1
posteroventral putamen R1
precentral gyrus L1
precentral gyrus R1
precuneus L1
precuneus R1
preoptic region of HTH L1
preoptic region of HTH R1
pretectal region L1
pretectal region R1
pulvinar of thalamus L1
pulvinar of thalamus R1
putamen L1
putamen R1
pyramidal part of medulla oblongata L1
pyramidal part of medulla oblongata R1
red nucleus L1
red nucleus R1
reuniens nucleus medioventral nucleus of thalamus L1
reuniens nucleus medioventral nucleus of thalamus R1
rostral gyrus L1
rostral gyrus R1
septal nuclei L1
septal nuclei R1
short insular gyri L1
short insular gyri R1
subcallosal gyrus parolfactory gyrus L1
subcallosal gyrus parolfactory gyrus R1
substantia nigra L1
substantia nigra R1
subthalamic nucleus L1
subthalamic nucleus R1
superior cerebellar peduncle brachium conjunctivum L1
superior cerebellar peduncle brachium conjunctivum R1
superior colliculus L1
superior colliculus R1
superior frontal gyrus L1
superior frontal gyrus R1
superior occipital gyrus L1
superior occipital gyrus R1
superior temporal gyrus L1
superior temporal gyrus R1
supramarginal gyrus L1
supramarginal gyrus R1
supraoptic region of HTH L1
supraoptic region of HTH R1
supraparietal lobule L1
supraparietal lobule R1
tail of caudate L1
tail of caudate R1
tail of hippocampus L1
tail of hippocampus R1
tegmentum of medulla oblongata L1
tegmentum of medulla oblongata R1
temporal agranular insular cortex area Tl L1
temporal agranular insular cortex area Tl R1
temporal pole L1
temporal pole R1
thalamus L1
thalamus R1
third ventricle L1
third ventricle R1
transverse temporal gyrus Heschls gyrus L1
transverse temporal gyrus Heschls gyrus R1
tuberal region of HTH L1
tuberal region of HTH R1
ventral anterior nucleus of thalamus L1
ventral anterior nucleus of thalamus R1
ventral lateral nucleus of thalamus L1
ventral lateral nucleus of thalamus R1
ventral posterior lateral nucleus L1
ventral posterior lateral nucleus R1
ventral posterior medial nucleus L1
ventral posterior medial nucleus R1
white matter of forebrain L1
white matter of forebrain R1
white matter of hindbrain L1
white matter of hindbrain R1
zona incerta L1
zona incerta R1
Male: Heart Details
3D Model: Heart, Male
Anatomical Structure ID Count
# Anatomical Structures 15
heartUBERON:00009481
aortic valveUBERON:00021371
heart left ventricleUBERON:00020841
heart right ventricleUBERON:00020801
interventricular septumUBERON:00020941
left cardiac atriumUBERON:00020791
mitral valveUBERON:00021351
papillary muscle of heartUBERON:00024945
pulmonary valveUBERON:00021461
right cardiac atriumUBERON:00020781
tricuspid valveUBERON:00021341
Female: Heart Details
3D Model: Heart, Male
Anatomical Structure ID Count
# Anatomical Structures 15
heartUBERON:00009481
aortic valveUBERON:00021371
heart left ventricleUBERON:00020841
heart right ventricleUBERON:00020801
interventricular septumUBERON:00020941
left cardiac atriumUBERON:00020791
mitral valveUBERON:00021351
papillary muscle of heartUBERON:00024945
pulmonary valveUBERON:00021461
right cardiac atriumUBERON:00020781
tricuspid valveUBERON:00021341
Male: Intestine, Large Details
3D Model: Large Intestine, Male
Anatomical Structure ID Count
# Anatomical Structures 11
large intestineUBERON:00000591
Ascending Colon UBERON:0001156 1
Caecum UBERON:0001153 1
Descending Colon UBERON:0001158 1
Hepatic Flexure of Colon UBERON:0022277 1
Ileocecal Valve UBERON:0000569 1
Rectum UBERON:0001052 1
Sigmoid Colon UBERON:0001159 1
Splenic Flexure of Colon UBERON:0022276 1
Transverse Colon UBERON:0001157 1
Vermiform Appendix UBERON:0001154 1
Female: Intestine, Large Details
3D Model: Large Intestive, Female
Anatomical Structure ID Count
# Anatomical Structures 11
large intestineUBERON:00000591
Ascending Colon UBERON:0001156 1
Caecum UBERON:0001153 1
Descending Colon UBERON:0001158 1
Hepatic Flexure of Colon UBERON:0022277 1
Ileocecal Valve UBERON:0000569 1
Rectum UBERON:0001052 1
Sigmoid Colon UBERON:0001159 1
Splenic Flexure of Colon UBERON:0022276 1
Transverse Colon UBERON:0001157 1
Vermiform Appendix UBERON:0001154 1
Male: Kidney, L Details
3D Model: Kidney, Male, Left
Anatomical Structure ID Count
# Anatomical Structures 39
kidneyUBERON:00021131
cortex of kidney UBERON:0001225 1
hilum of kidney UBERON:0008716 1
kidney capsule UBERON:0002015 1
major calyx UBERON:0001226 3
minor calyx UBERON:0001227 9
outer cortex of kidney UBERON:0002189 1
renal column UBERON:0001284 1
renal medulla UBERON:0000362 1
renal papilla UBERON:0001228 9
renal pelvis UBERON:0001224 1
renal pyramid UBERON:0004200 9
ureter UBERON:0001223 1
Artery 1
Veins 1
Male: Kidney, R Details
3D Model: Kidney, Male, Right
Anatomical Structure ID Count
# Anatomical Structures 40
kidneyUBERON:00021131
cortex of kidney UBERON:0001225 1
hilum of kidney UBERON:0008716 1
kidney capsule UBERON:0002015 1
major calyx UBERON:0001226 2
minor calyx UBERON:0001227 9
outer cortex of kidney UBERON:0002189 1
renal column UBERON:0001284 1
renal medulla UBERON:0000362 1
renal papilla UBERON:0001228 10
renal pelvis UBERON:0001224 1
renal pyramid UBERON:0004200 10
ureter UBERON:0001223 1
Artery 1
Veins 1
Female: Kidney, L Details
3D Model: Kidney, Male, Right
Anatomical Structure ID Count
# Anatomical Structures 45
kidneyUBERON:00021131
cortex of kidney UBERON:0001225 1
hilum of kidney UBERON:0008716 1
kidney capsule UBERON:0002015 1
major calyx UBERON:0001226 4
minor calyx UBERON:0001227 10
outer cortex of kidney UBERON:0002189 1
renal column UBERON:0001284 1
renal medulla UBERON:0000362 1
renal papilla UBERON:0001228 11
renal pelvis UBERON:0001224 1
renal pyramid UBERON:0004200 1
ureter UBERON:0001223 1
Artery 1
Veins 1
Female: Kidney, R Details
3D Model: Kidney, Male, Right
Anatomical Structure ID Count
# Anatomical Structures 42
kidneyUBERON:00021131
cortex of kidney UBERON:0001225 1
hilum of kidney UBERON:0008716 1
kidney capsule UBERON:0002015 1
major calyx UBERON:0001226 4
minor calyx UBERON:0001227 10
outer cortex of kidney UBERON:0002189 1
renal column UBERON:0001284 1
renal medulla UBERON:0000362 1
renal papilla UBERON:0001228 11
renal pelvis UBERON:0001224 1
renal pyramid UBERON:0004200 11
ureter UBERON:0001223 1
Artery 1
Veins 1
Male: Lung, L Details
3D Model: Lung, Male, Left
Anatomical Structure ID Count
# Anatomical Structures 82
lungUBERON:00020481
arytenoid cartilageUBERON:00017401
arytenoid muscleUBERON:00109581
carina of tracheaFMAID:74651
corniculate cartilageFMAID:551101
crico-arytenoid muscleUBERON:00109321
cricoid cartilageFMAID:96151
epiglottic cartilageFMAID:551121
inferior lingular bronchopulmonary segmentFMAID:73751
inferior lingular bronchusFMAID:74311
interlobar bronchusFMAID:74151
lateral segmental bronchusFMAID:74021
left anterior basal bronchopulmonary segmentFMAID:73781
left anterior basal segmental bronchusFMAID:75061
left anterior Bronchopulmonary SegmentFMAID:73731
left anterior segmental bronchusFMAID:74281
left apical bronchopulmonary segmentFMAID:73851
left apical segmental bronchusFMAID:74261
left arytenoid cartilageFMAID:551141
left corniculate cartilageFMAID:551161
left Lateral Basal Bronchopulmonary SegmentFMAID:73791
left lateral basal segmental bronchusFMAID:75071
left lung hilusUBERON:00048871
left main BronchusUBERON:00021781
left medial Basal Bronchopulmonary SegmentFMAID:73771
left medial basal segmental bronchusFMAID:75051
left posterior basal bronchopulmonary segmentFMAID:73801
left posterior basal segmental bronchusFMAID:75081
left posterior bronchopulmonary segmentFMAID:73861
left superior bronchopulmonary segmentFMAID:73761
left superior segmental bronchusFMAID:75041
lobar bronchus of left lungUBERON:00034051
lobar bronchus of left lung lower lobeUBERON:00120661
lobar bronchus of left lung upper lobeUBERON:00120651
lobar bronchus of right lungUBERON:00034041
lower Lobe of left LungUBERON:00089531
medial segmental bronchusFMAID:74031
middle lobar bronchusFMAID:74011
middle Lobe of right LungUBERON:00021741
muscle fasciculus of lateral crico-arytenoidFMAID:477671
Muscle fasciculus of left lateral crico-arytenoidFMAID:477691
Muscle fasciculus of left posterior crico-arytenoidFMAID:477541
Muscle fasciculus of right lateral crico-arytenoidFMAID:477681
Muscle fasciculus of right posterior crico-arytenoidFMAID:477531
posterior crico-arytenoidUBERON:00085721
right anterior basal bronchopulmonary segmentFMAID:73641
right anterior basal segmental bronchusFMAID:74181
right Anterior Bronchopulmonary SegmentFMAID:73591
right anterior segmental bronchusFMAID:74001
right Apical Bronchopulmonary SegmentFMAID:73381
right apical segmental bronchusFMAID:73981
right arytenoid cartilageFMAID:551131
right corniculate cartilageFMAID:551151
right inferior lobar bronchusFMAID:74041
right Lateral Basal Bronchopulmonary SegmentFMAID:73631
right lateral basal segmental bronchusFMAID:74191
right Lateral Bronchopulmonary SegmentFMAID:73611
right lung hilusUBERON:00048881
Male: Lung, R Details
3D Model: Lung, Male, Right
Anatomical Structure ID Count
# Anatomical Structures 44
lungUBERON:00020481
carina of tracheaFMAID:74651
cricoid cartilageFMAID:96151
epiglottic cartilageFMAID:551121
inferior lingular bronchopulmonary segmentFMAID:73751
left anterior basal bronchopulmonary segmentFMAID:73781
left Anterior Bronchopulmonary SegmentFMAID:73735
left apical bronchopulmonary segmentFMAID:73851
Left arytenoid cartilageFMAID:551141
Left corniculate cartilageFMAID:551161
left Lateral Basal Bronchopulmonary SegmentFMAID:73791
left lung hilusUBERON:00048871
Left Main BronchusUBERON:00021781
Left Medial Basal Bronchopulmonary SegmentFMAID:73771
Left posterior basal bronchopulmonary segmentFMAID:73801
Left posterior bronchopulmonary segmentFMAID:73861
Left superior bronchopulmonary segmentFMAID:73761
Lower Lobe of Left LungUBERON:00089531
Lower Lobe of Right LungUBERON:00021711
Middle Lobe of Right LungUBERON:00021741
Right anterior basal bronchopulmonary segmentFMAID:73641
Right Anterior Bronchopulmonary SegmentFMAID:73591
Right Apical Bronchopulmonary SegmentFMAID:73381
Right arytenoid cartilageFMAID:551131
Right corniculate cartilageFMAID:551151
Right Lateral Basal Bronchopulmonary SegmentFMAID:73631
Right Lateral Bronchopulmonary SegmentFMAID:73611
right lungUBERON:00021671
right lung hilusUBERON:00048881
Right Main BronchusUBERON:00021771
Right Medial Basal Bronchopulmonary SegmentFMAID:73651
Right Medial Bronchopulmonary SegmentFMAID:73601
Right Posterior Basal Bronchopulmonary SegmentFMAID:73621
Right Posterior Bronchopulmonary SegmentFMAID:73391
Right Superior Bronchopulmonary SegmentFMAID:73661
Superior lingular bronchopulmonary segmentFMAID:73741
Thyroid cartilageFMAID:550991
tracheaUBERON:00031261
Upper Lobe of Left LungUBERON:00089521
Upper Lobe of Right LungUBERON:00021701
Female: Lung, L Details
3D Model: Lung, Female, left
Anatomical Structure ID Count
# Anatomical Structures 25
lungUBERON:00020481
arytenoid cartilage l1
arytenoid cartilage r1
carina1
corniculate cartilage l1
corniculate cartilage r1
cricoid cartilage1
epiglottic cartilage1
hilum l1
hilum lower l1
hilum upper l1
left anterior basal bronchopulmonary segment1
left anterior bronchopulmonary segment1
left apical bronchopulmonary segment1
left lateral basal bronchopulmonary segment1
left lingular inferior bronchopulmonary segment1
left lingular superior bronchopulmonary segment1
left main bronchus1
left medial basal bronchopulmonary segment1
left posterior basal bronchopulmonary segment1
left posterior bronchopulmonary segment1
left superior bronchopulmonary segment1
right main bronchus1
thyroid cartilage1
trachea1
Female: Lung, R Details
3D Model: Lung, Female, Right
Anatomical Structure ID Count
# Anatomical Structures 25
lungUBERON:00020481
arytenoid cartilage l1
arytenoid cartilage r1
carina1
corniculate cartilage l1
corniculate cartilage r1
cricoid cartilage1
epiglottic cartilage1
hilum lower r1
hilum middle r1
hilum upper1
left main bronchus1
right anterior basal bronchopulmonary segment1
right anterior bronchopulmonary segment1
right apical bronchopulmonary segment1
right lateral basal bronchopulmonary segment1
right lateral bronchopulmonary segment1
right main bronchus1
right medial basal bronchopulmonary segment1
right medial bronchopulmonary segment1
right posterior basal bronchopulmonary segment1
right posterior bronchopulmonary segment1
right superior bronchopulmonary segment1
thyroid cartilage1
trachea1
Male: Lymph Node, L Details
3D Model: Lymph Node, Left, Male
Anatomical Structure ID Count
# Anatomical Structures 8
lymph nodeUBERON:00000291
afferent lymphatic vesselUBERON:00103961
capsule of lymph nodeUBERON:00021941
efferent lymph nodeUBERON:00103971
lymph node cortexUBERON:00107481
medulla of lymph nodeUBERON:00020071
paracortex (lymph node T cell domain)UBERON:00104171
vasculature1
Male: Lymph Node, R Details
3D Model: Lymph Node, Right, Female
Anatomical Structure ID Count
# Anatomical Structures 8
lymph nodeUBERON:00000291
afferent lymphatic vesselUBERON:00103961
capsule of lymph nodeUBERON:00021941
efferent lymph nodeUBERON:00103971
lymph node cortexUBERON:00107481
medulla of lymph nodeUBERON:00020071
paracortex (lymph node T cell domain)UBERON:00104171
vasculature1
Female: Lymph, L Details
3D Model: Lymph Node, Left, Female
Anatomical Structure ID Count
# Anatomical Structures 8
lymph nodeUBERON:00000291
afferent lymphatic vesselUBERON:00103961
capsule of lymph nodeUBERON:00021941
efferent lymph nodeUBERON:00103971
lymph node cortexUBERON:00107481
medulla of lymph nodeUBERON:00020071
paracortex (lymph node T cell domain)UBERON:00104171
vasculature1
Female: Lymph Node, R Details
3D Model: Lymph Node, Right, Female
Anatomical Structure ID Count
# Anatomical Structures 8
lymph nodeUBERON:00000291
afferent lymphatic vesselUBERON:00103961
capsule of lymph nodeUBERON:00021941
efferent lymph nodeUBERON:00103971
lymph node cortexUBERON:00107481
medulla of lymph nodeUBERON:00020071
paracortex (lymph node T cell domain)UBERON:00104171
vasculature1
Male: Skin Details
3D Model: Skin, Male
Anatomical Structure ID Count
# Anatomical Structures 1
skin of body UBERON:0002097 1
Female: Skin Details
3D Model: Skin, Female
Anatomical Structure ID Count
# Anatomical Structures 1
skin of body UBERON:0002097 1
Male: Spleen Details
3D Model: Kidney, Male, Left
Anatomical Structure ID Count
# Anatomical Structures 6
spleenUBERON:00021061
colic surface of spleenFMAID:158381
diaphragmatic surface of spleenFMAID:158281
gastric surface of spleenFMAID:158371
hilum of spleenUBERON:00012481
renal surface of spleenFMAID:158391
Female: Spleen Details
3D Model: Kidney, Male, Left
Anatomical Structure ID Count
# Anatomical Structures 6
spleenUBERON:00021061
colic surface of spleenFMAID:158381
diaphragmatic surface of spleenFMAID:158281
gastric surface of spleenFMAID:158371
hilum of spleenUBERON:00012481
renal surface of spleenFMAID:158391
Male: Thymus Details
3D Model: Kidney, Male, Left
Anatomical Structure ID Count
# Anatomical Structures 2
thymusUBERON:00023701
thymus lobe L UBERON:0005457 1
thymus lobe R UBERON:0005469 1
Female: Thymus Details
3D Model: Thymus, Female
Anatomical Structure ID Count
# Anatomical Structures 3
thymusUBERON:00023701
thymus lobe L UBERON:0005457 1
thymus lobe R UBERON:0005469 1
Male: Vasculature Details
3D Model: Vasculature, Male
Anatomical Structure ID Count
# Anatomical Structures 81
vasculatureUBERON:00020491
anterior cardiac veinFMAID:767671
anterior interventricular branch of left coronary arteryFMAID:38621
aortaUBERON:00009471
arch of aortaUBERON:00015081
ascending aortaUBERON:00014961
brachiocephalic arteryUBERON:00015292
brachiocephalic veinUBERON:00037111
cardiac arteries1
cardiac veinUBERON:00041481
celiac arteryUBERON:00016401
circumflex branch of left coronary arteryUBERON:00354221
colic arteryUBERON:00355481
common iliac veinUBERON:00011391
coronary sinusUBERON:00054381
descending aortaUBERON:00015142
diagonal branch of anterior descending branch of left coronary arteryFMAID:38601
external iliac veinUBERON:00013161
great vein of heartUBERON:00069581
ileocolic arteryUBERON:00355481
ileocolic veinUBERON:00012191
inferior mesenteric arteryUBERON:00011831
inferior mesenteric veinUBERON:00012151
inferior pancreaticoduodenal veinUBERON:00113831
inferior rectal veinFMAID:212422
inferior vena cavaFMAID:109512
internal iliac veinUBERON:00013172
internal pudendal veinUBERON:00182522
left colic arteryFMAID:148261
left colic veinFMAID:153941
left common carotid artery plus branchesUBERON:00015362
left common iliac veinFMAID:213881
left coronary arteryUBERON:00016261
left subclavian arteryUBERON:00015841
marginal branch of right coronary arteryFMAID:38181
median sacral veinUBERON:00066871
middle cardiac veinUBERON:00096871
middle colic arteryUBERON:00011961
middle colic veinUBERON:00012181
middle rectal veinFMAID:188932
oblique vein of left atriumFMAID:47151
hepatic portal veinUBERON:00016391
posterior vein of left ventricleFMAID:47121
pulmonary arteryUBERON:00020121
pulmonary trunkUBERON:00023331
pulmonary veinUBERON:00020164
renal arteryUBERON:00011842
renal veinUBERON:00011402
right colic arteryFMAID:148111
right colic veinFMAID:154071
right common iliac veinFMAID:213871
right coronary arteryUBERON:00016251
right posterior descending arteryFMAID:38401
sigmoid arteryUBERON:00351801
sigmoid veinFMAID:153953
small cardiac veinUBERON:00353741
splenic arteryUBERON:00011942
splenic veinUBERON:00037131
superior mesenteric arteryUBERON:00011823
superior mesenteric veinUBERON:00011381
superior rectal veinFMAID:153931
superior vena cavaFMAID:47201
vena cavaUBERON:00040871
Female: Vasculature Details
3D Model: Vasculature, Female
Anatomical Structure ID Count
# Anatomical Structures 81
vasculatureUBERON:00020491
anterior cardiac veinFMAID:767671
anterior interventricular branch of left coronary arteryFMAID:38621
aortaUBERON:00009471
arch of aortaUBERON:00015081
ascending aortaUBERON:00014961
brachiocephalic arteryUBERON:00015292
cardiac veinUBERON:00041481
celiac arteryUBERON:00016401
circumflex branch of left coronary arteryUBERON:00354221
colic arteryUBERON:00355481
common iliac veinUBERON:00011391
coronary sinusUBERON:00054381
descending aortaUBERON:00015142
diagonal branch of anterior descending branch of left coronary arteryFMAID:38601
great vein of heartUBERON:00069581
ileocolic arteryUBERON:00355481
ileocolic veinUBERON:00012191
inferior mesenteric arteryUBERON:00011831
inferior mesenteric veinUBERON:00012151
inferior pancreaticoduodenal veinUBERON:00113831
inferior rectal veinFMAID:212422
inferior vena cavaFMAID:109512
internal iliac veinUBERON:00013172
internal pudendal veinUBERON:00182522
left colic arteryFMAID:148261
left colic veinFMAID:153941
left common carotid artery plus branchesUBERON:00015362
left common iliac veinFMAID:213881
left coronary arteryUBERON:00016261
left marginal veinFMAID:47081
left posterior descending branch of circumflex branch of left coronary arteryFMAID:3229041
left subclavian arteryUBERON:00015842
marginal branch of right coronary arteryFMAID:38181
median sacral veinUBERON:00066871
middle cardiac veinUBERON:00096871
middle colic arteryUBERON:00011961
middle colic veinUBERON:00012181
middle rectal veinFMAID:188932
oblique vein of left atriumFMAID:47151
hepatic portal veinUBERON:00016391
Posterior ventricular branch of circumflex coronary arteryFMAID:139051
posterior vein of left ventricleFMAID:47121
pulmonary arteryUBERON:00020122
pulmonary trunkUBERON:00023331
pulmonary veinUBERON:00020164
renal arteryUBERON:00011842
renal veinUBERON:00011402
right colic arteryFMAID:148111
right colic veinFMAID:154071
right common iliac veinFMAID:213871
right coronary arteryUBERON:00016251
sigmoid arteryUBERON:00351803
sigmoid veinFMAID:153953
small cardiac veinUBERON:00353741
splenic arteryUBERON:00011941
splenic veinUBERON:00037131
superior mesenteric arteryUBERON:00011821
superior mesenteric veinUBERON:00011381
superior rectal arteryFMAID:153931

Acknowledgements

The 3D Models were created by Kristen Browne for the 3D Printing and Biovisualization program operated by OCICB, NIAID. This research has been funded in part by the NIH Common Fund through the Office of Strategic Coordination/Office of the NIH Director under award OT2OD026671, by the NIDDK Kidney Precision Medicine Project grant U2CDK114886, and NIAID under BCBB Support Services Contract HHSN316201300006W/HHSN27200002 to MSC, Inc; U.S.

The male colon is from a white 55-year-old and was provided by Arie Kaufman, Stony Brook University.

The brain is from a 34‐year‐old female donor and was published by the Allen Human Reference Atlas–3D, 2020. Jim Gee, University of Pennsylvania converted the NII file into GLB. Amy Bernard, Allen Institute assisted in mapping the 141 anatomical structures to the brain ASCT+B table.

References

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  • Ding, Song-Lin, Joshua J. Royall, Susan M. Sunkin, Benjamin A.C. Facer, Phil Lesnar, Amy Bernard, Lydia Ng, and Ed S. Lein. 2020. Allen Human Reference Atlas – 3D, 2020. RRID:SCR_017764, version 1.0.0.
  • U.S. National Library of Medicine. 2021. Visible Human Project Data.

March 22, 2021