Welcome to BodyParts3D.

Contents

Information

  • Welcome to BodyParts3D/Anatomography.
  • BodyParts3D is an anatomical dictionary where terms are defined by 3D morphology of referents.
  • BodyParts3D serves as a kit to build custom 3D manikins.
  • We plan to define all anatomical concepts listed in Terminologia Anatomica, started from those with volumes. <link to stat>
  • Anatomography is a web application that enables users to build and publish own custom manikins.
Map examples for reuse

For repeaters

Notice

IMPORTANT MESSAGE TO USERS

  • There are still many concepts not represented in the data.
  • There could be many ERRORS to be used as ANATOMICAL EDUCATION.
    • Some parts were made from scratch by artists or distorted to fit into the environment.
    • Segmentation into finer pieces may cause confusion in assignment of concepts.
  • Authors may publish your models at your own risk of inclusion of such errors.
  • For notion and improvement, please feed back and share the PROBLEMS YOU FIND in the data.
  • Started from the provided TWITTER function in the BodyParts CARD (right side window) The SUBJECT of the comment ( parts form or its concept label) will be recorded automatically and properly distributed.
  • Your cooperation will be truly appreciated. -- BodyParts3D team

Whats new

  • New data release: Now (April 15, 2014), peripheral nerves and cranial vessels are under inspection and concept mapping. They will be released in a month as version 5.0.
  • Old news and Notices [1]
   2012/06/21: BodyParts3D rel 4.0 downloadable as a whole from LSDB archive.
   2013/05/16: BodyParts3D rel 4.0 from Editor site. major update for map editor site
   2011/06/20: BodyParts3D 3.0 published from editor site release note to rel. 3.0
   2010/08/16: data download service at LSDB archive: all Rel.2.0 obj files
   2010/07/21: BodyParts3D release 2.0 modeling note
   2010/04/28: BodyParts3D release 2.0 with new editor site。release note to rel. 2.0(概要)

For new visitors

What is this site about? (Map editor)

  • What you can do with BodyParts3D/Anatomography [2]
  • How to use : tutorial ftg on youtube
 
    • Bodyparts3D map editor site UI details[3]
    • Step by step, how to use[4]

Web API behind

Data download

image with coordinates by Will Robertson (http://wspr.wordpress.com/)

License

  • Users can copy modify and disseminate both contour data and rendered image under the license CC-BY SA 2.1JP

sample html source here ..

http://dbarchive.biosciencedbc.jp/en/bodyparts3d/lic.html

Introducing team and Project (Who are we)

  • Personel:

<BodyParts3D>

    • Parts data generation : Kaori Fujieda
    • Parts data generation :Shio Imai
    • Parts concept mapping (environment):Nobutaka Mitsuhashi, Isamu Muto
    • Parts concept mapping (operation): Kousaku Okubo, M.D.
    • DICOM processing: Nobutaka Mitsuhashi, Kaori Fujieda
    • Anatomy information environment:
    • Rationale and Project Design:Kousaku Okubo

<Anatomography>

    • Rationale and Project Design:Kousaku Okubo
    • Implementation design:Takuro Tamura,Nobutaka Mitsuhashi, Isamu Muto
    • Implementation: Nobutaka Mitsuhashi, Bits c.c.
    • System maintainance: DBCLS, NBDC
  • Funding Source: MEXT, JST
  • Institutional background: DBCLS,
  • Out sourcing:

For those who care (How dose this work)

About Anatomography (mechanism of authoring site)

  • Whole Diagram

BPAT1.PNG

  • For those who cares very much (designed and depicted by Isamu Muto, Bits c.c.)

SYSTEM.PNG

  • Data management:Representation and contour file, Versions, Search, Menu
  • About API mechanism

About BodyParts3D data

Processes for modelling

  • How do we made contour data
    • Modelling note
    • Contour concept mapping HOW DO I MAP OBJ DATA TO FMA CONCEPT [6]
    • Primary Mapping results {one object(FJ) to one FMA} [7]
    • Mapping result expanded by FMA relations{one FMA to component Obj files(FJ)}
    • Data types (Compound and elementary)

Data types

  1. Artists make 3D contour of body parts from scratch or modification of clinical 3D images, scanned plastic models, with reference to anatomical textbooks, atlases and other image sources.
  2. This ELEMENTAL DATA(primitive.png) is mapped to the corresponding , or the closest concept chosen from FMA.
  3. Form the side of concept mapping concept to contour is called representation.
  4. Those mapped ELEMENTALS are re-used in generating logical aggregation of contour data for higher order concepts .
  5. For this purpose ontological relations of concepts provided from out-side of the project , at this moment FMA, is used. (build-up contour; build-up concept)
  6. Accordingly, the same concept may be represented by different COMPOUND DATA (075.png) depending on the choice of the logic.
  7. For example, big organ have only COMPOUND contour in part-of logic but no is-a contor because it dose dot have categorical subordinates.
  8. Representation have two types; ELEMENTAL/DIRECT representation and COMPOUND/SECONDARYrepresentation.
  9. COMPOUND representation may be complete(100.png) in some cases such as "left hand+right hand-->hands".
  10. But in most cases, only a subset of subordinate concept have "ELEMENTAL DATA.
  11. In such cases, representation has a feature called representation density.
  12. The ration of represented subordinate concepts and all subordinate concepts in COMPOUND is density shown by red/white Pie.

Heart tree.jpg  

  1. Build-up Representation of mandibula with FMA:Part-OF logic. IN bp3.0 data, with fma3.0 part-of logic, build-up representation density for FMA7485:Mandibura, is 3/7 .

Data stats & Release Hx

  • Stats in concept number

In the present version, relations of logic and contour representation s are as follows. [10]

bp3d_v2.0	FMA concepts	ELEMENTAL COMPOUND 
is-a tree	80457	843	643
part-of tree	35597	408	326
in both tree	30068	406	0
all unique FMA	80457	845	969
bp3d_v3.0	FMA concepts	ELEMENTAL COMPOUND 
is-a tree	80457	912	700
part-of tree	35597	436	353
in both tree	30068	433	0
all unique FMA	80457	915	1053
bp3d_v4.0	FMA concepts	ELEMENTAL 	COMPOUND 
is-a tree	80457	1651	1254
part-of tree	35597	765	603
in both tree	30068	764	3
all unique FMA	80457	1652	1854
	                        TA	FMA				
Material Anatomical Entity	460y1	4600				
Inmaterial Anatomical Entity	2238	2306		
※obj有無に関係無くTA-FMA対応がある数		
						
						
Material Anatomical Entity TA:4601
	           IS-A			PART-OF		
  	      V2	V3	V4	V2	V3	V4
element	        96	99	211	63	73	137
compound	299	334	514	66	74	161
						
Material Anatomical Entity	IS-A			PART-OF		
FMA:4600	V2	V3	V4	V2	V3	V4
element	93	98	207	63	72	133
compound	293	325	499	63	71	160
						
						
Inmaterial Anatomical Entity  TA:2238	
             IS-A			PART-OF		
	      V2	V3	V4	V2	V3	V4
element	      12	17	22	0	0	0
compound      10	12	14	5	5	5
						
Inmaterial Anatomical Entity FMA:2306
	     IS-A			PART-OF		
	      V2	V3	V4	V2	V3	V4
element	      12	17	21	0	0	0
compound	8	10	12	5	5	5
  • Release 4.0 (2013/5) Release Note (2013/5)
  • Release 3.0 (2011/6/20)
    • Release Note (2011/6/20)
    • Release Note (2010/4/28)
    • Modeling Note (PDF)(2010/7/21)
    • BodyParts3D Origin and insertion of skeletal muscles (Excel)(2010/8/30)
  • Release 1.0 (2009/2/9) [11]

Outside Resources

FMA Foundation model of Anatomy of Wahington-U

  • Rosse C, Mejino JL, Modayur BR, Jakobovits R, Hinshaw KP, Brinkley JF. Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist Symbolic Knowledge Base. J Am Med Inform Assoc. 1998;5:17–40.
  • Extraction from AMIA Annu Symp Proc. 2003; 2003: 450–454.PMCID: PMC1480337 Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy by José L.V. Mejino, Jr, MD, Augusto V. Agoncillo, MD, Kurt L. Rickard, PhD, and Cornelius Rosse, MD, DSc [12]

Terms in FMA

  • Constitutional part is a primary partition of an anatomical structure into its compositionally distinct anatomical elements.
  • In the context of the whole, an element is any relatively simple component of which a larger, more complex anatomical structure is compounded; i.e., the partition is compositional rather than spatial.
  • Regional part is a primary partition that spatially subdivides an anatomical structure into sets of diverse constitutional parts that share a given location within the whole; i.e., the partition is spatial rather than compositional.
  • Entities in all subclasses of Anatomical structure have both constitutional and regional parts, as illustrated by the following

examples:

    • Neuron -has constitutional part-Plasma membrane, Protoplasm;
    • Neuron-has regional part-Cell body, Axon, Dendrite;
    • Lung -has constitutional part- Visceral pleura, Lung parenchyma, Intrapulmonary airway, Vasculature, Neural network;
    • Lung -has regional part- Lobe of lung;Lobe of lung -has constitutional part- Visceral pleura, Lung parenchyma etc.;
  • Part-whole relationships are valid only for entities of the same dimension;
  • boundary relationships are valid for entities that differ by one in their dimensionality.

Accordingly, the following are valid assertions:

    • Right ventricle -has part- Wall of right ventricle, Cavity of right ventricle (3D anatomical entities);
    • Surface of heart -has part- Diaphragmatic surface of heart (2D entities); and
    • Surface of heart -bounds- Heart (2D and 3D entities, respectively). [13]

Terminologia Anatomica

    • Short introduction and link
  • TA contains terminology for about 7500 human gross (macroscopic) anatomical structures, while TH contains terminology for cellular structures, tissue and organs at the microscopic level. [14]
Terminologia Anatomica (TA) is the international standard on human anatomic terminology. It was developed by the Federative Committee on Anatomical Terminology (FCAT) and the International Federation of Associations of Anatomists (IFAA) and was released in 1998.[1] It supersedes the previous standard, Nomina Anatomica.[2] Terminologia Anatomica contains terminology for about 7500 human gross (macroscopic) anatomical structures.[3] In April 2011, Terminologia Anatomica was published online by the Federative International Programme on Anatomical Terminologies (FIPAT), the successor of FCAT. [15]

http://en.wikipedia.org/wiki/Terminologia_anatomica

Funato's Japanses translation digital text @ Keiko Univ. Med.Schl.

http://www.anatomy.med.keio.ac.jp/funatoka/TA.html

Image templates and reference

    • Taro
    • Stanford
    • MAI
    • Talairach
  • Reference books heavily used
    • FENEIS
    • FUNATO's site
    • RauberKopsch
  • Reference 3D data and sites
    • Visible
    • BodyBrowser
    • Lung CD

Terminology, references, random QA, Tips

Terminology

  1. Concept have FMAID (mostly), and contour data (=3D polygon files = obj files). They are different entities.
  2. A relation of concept/FMA1234 and contour data/FJ3456.obj is called Representation.
  3. Since representation may change time to time, we put representation ID "BP1234" for these paired ID.
  4. Representation have two types; ELEMENTAL/DIRECT representation and COMPOUND/SECONDARY representation.
  5. A contour data file made by artist is referred to as: ELEMENTAL DATAdenoted by red target in icon (image here)
  6. Concept manually mapped with one ELEMENTAL DATAfor its sufficient representation is: ELEMENTAL/DIRECTLY represented concept
  7. Contour file made operationally by joining one or more ELEMENTAL DATA according to the provided tree of concepts are: COMPOUND/SECONDARY represented DATA; COMPOUNDS. denoted by red/white pie (image here)
  8. The ratio of existing part and missing part in COMPOUND is shown by red/white Pie.
  • About representation, concept,

More infromation sources

  • Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, and Kousaku Okubo BodyParts3D: 3D structure database for anatomical concepts Nucleic Acids Research, 2009, Vol. 37, Database issue D782-D785, DOI 10.1093/nar/gkn613.
  • Presentations BMB2009| BMB2008| BMB2007
  • Seminars (AJACS) 2010年度: AJACSみちのく(2010/8)| AJACS and DDBJing in 東京(2010/6)| AJACS湘南2(2010/6) 2009年度: AJACSりんくう(2009/11)| AJACS近江2(2009/10)| AJACS三河(2009/7) 2008年度: AJACS長津田(2009/1)| AJACS近江| AJACS博多| AJACS本郷1
  • Symposium 「データベースが拓くこれからのライフサイエンス」(2009/6/21) [16]

Embed in Third parties

Dissemination status

図1.png

Systematic use of API from programs( General, Molecular and Clinical)

<iframe frameborder="0" webkitallowfullscreen="" mozallowfullscreen="" allowfullscreen="" width="550" height="400" src="http://prezi.com/embed/vmwtuw_ije71/?bgcolor=ffffff&lock_to_path=0&autoplay=0&autohide_ctrls=0#"></iframe>

3D data use (Physiome research, Diagnostic, Clinical devices, Education)

Downloads and Mirrors for CAD and 3D printing community

Image use

Scholarly journals

NEDO.JPG

MEDIA

1344680655_ihnwy.jpg

3rd party delivations

skeletoncover01.bmp0c0eb295-1e0f-4a4f-81f6-cad046f86efaLarge.jpg

システム解説

BPAT1.PNG

  • BodyParts3D/Anatomography サービスはウエブアプリケーション(BodyParts3Dサイト + アナトモグラフィーサイト) および アナトモグラフィーウエブ-API を通じて 利用者のweb ブラウザー または カスタムプログラム に対して ボディーパーツ情報およびマップデータを提供しています。
  • BodyParts3D サイトは登録パーツデータベースを検索するためのウエブアプリケーションです
  • アナトモグラフィーサイトはマップエディター機能を提供するアナトモグラフィーウエブ-API 上のウエブアプリケーションです。
  • アナトモグラフィーウエブAPIはOpenGLにかぶさったウエブAPIで、リクエストに対してイメージデータおよびマップデータ要素を返します。
  • それぞれの構成は以下のようになっています。

SYSTEM.PNG

提供データソース

  • パーツデータのメタ情報:
    • データアイコン: 3Dパーツデータが更新されるとプログラム的に作成しなおします(ビッツ)
    • データファイル名称と概念名称の対応:3Dパーツデータ更新時に作成します(大久保)
    • 概念間の関係(FMA) および概念の呼称の辞書(FMA):FMA更新時に入れ替えます(ビッツ)
  • 3Dパーツデータ (obj ファイル): DBCLSから提供されます ビッツのwebGL系の編集サイトから大久保に提供され各ファイルに概念がマップされます
  • 前者は登録パーツデータベースで管理されBodyParts3Dサイトを通じて検索利用されます。
  • 後者はOpenGLに常にロードされており、ウエブAPIを通じて利用されます。

維持管理

  • ボディーパーツデータはいまだ付加更新中であるために 維持管理はデータ更新に伴うものと日々の利用上の管理があります。

データ更新に伴う管理

データ修正サイクル

  • Artsist がFFMで作ったデータはFMAマッピングの後でBAckStage Editor にOBJファイルとして登録されます。
  • Back stage で検出された形態上の誤りは ウィンドウズ環境で訂正され再度Back Stageにアップされます。
  • この際に特定のデータセットで利用するファイルを指定しなおします。(use with which set or not)
  • このステップが可能になったおかげでこれまで気づいていても放置されていた誤りがタイムリーに変更可能になります。

データ追加サイクル

  • FFMで作成していない詳細なデータがMeshMixerで作成され追加されます。

ex. Heart segmentation and coronary ex Limbic system Thalamus At the resolution of neurosciences