Forum Posts

Melodicpinpon
Biomechanist
Biomechanist
May 24, 2022
In About the anatomical content
Dear Anatomist, Several file formats of animals' skulls can be downloaded on the web under a CC-BY-SA license. These files, once integrated into the atlas environment, can easily be completed to become partial veterinary atlases. These resources are shared on: Phenom10K (.obj) Digimorph (high contrast scans as .jpg) Morphosource (scans) The importation of scans into Blender is a process that requires two or three steps and the use of a short script, but it is completely possible. The process could probably be automated with some more python scripting. Some experiments have been made to interact with these files: Boolean on scan Cross section planes on meshes These two files can be shared if required. Besides these models generated from medical scanners, a series of beautiful 3D skulls are shared (sktechfab, etc.) but, since they are produced with a surface scanner, and not a medical scanner, the internal walls and sinuses are not represented. Back to the CONTRIBUTORS' HOMEPAGE
How to create ANIMAL MODELS content media
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Melodicpinpon
Biomechanist
Biomechanist
May 24, 2022
In About the anatomical content
Dear Anatomist, Many demands have been received to create a female model. It is obviously on the to-do list but it raises specific technical issues. This post gathers the information about this aspect of the project. How can a female model be created? First, the male model is a modified version of 'BodyParts3D', created under CC-BY-SA license around 2012 by a Japanese team. The technique used to produce this model is a mystery: the original files seem to be generated from a segmentation of a .dicom (scan/IRM), but the body is in perfect position (no flesh squashing due to the horizontal position). The question has been asked to the author and received no answer for the moment. The visual quality of the atlas comes from this unknown technique: the overall shape is very natural and the fibers of each muscle are visible in the 3D mesh (the downside is that they are therefore heavier, and less texture-compatible). In order to create an anatomically accurate female model, we need: 1) A .dicom reference: It may already exist or have to be created. Getting a detailed .dicom of the whole body is somewhat unusual but the main obstacle is, in my opinion, to find out/decide which is the best technique to produce a 3D model in anatomical position (standing) from a scan/IRM done lying down. 2) Create or adapt the meshes to fit this reference: My proposition would be to transform the male model using the 'Lattice' modifier. All the objects, the names and the relationships of the common anatomical structures would be already available and could be influenced together. Much manual edition of the meshes and curves would then be needed to reach the final result. The final result could then be: -either another .blend file -or the same .blend file, with the same objects and meshes, but in other 'Shapekeys' This choice is a technical decision to take, based on the file size and memory (RAM) needed to navigate in the model (in Blender and in the mobile app). All this represent an important amount of work and more workers/resources/time would be needed. A solution would be to create a 3D model of the female anatomical structures and make a separate atlas of it. All the functions would be available. It could then be integrated later on, if/when the conditions to produce the whole open source female model are gathered. Back to the CONTRIBUTORS'HOMEPAGE
Create a FEMALE MODEL content media
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Melodicpinpon
Biomechanist
Biomechanist
May 23, 2022
In About Blender
Dear Biomechanist, As Blender -is meant to create animations -supports Armatures and constraints -supports Motion Capture files -allows to associate 3D shapes to the MoCap files, it provides an original approach for the study of biomechanics. To be influenced by the armature, the 3D objects are usually parented to the armature. As these parenthood relationships are already used to represent the hierarchy of anatomical structures in the main file -because this is how a hierarchy can be exported from Blender to Unity- the anatomy and the biomechanics had to be separated. You will find the 'Biomechanics Blender.7z' file, containing the armature, a series of positions and a few .bvh animations on the 'How To...' page of this website, beneath the button 'Armature'. Constraints were added to limit the body in physiologically coherent positions. A system has been developed to automate the animation of the whole skeleton using .bvh files (standard Motion Capture format). The reproduction of the physiological movements in Blender implies a good understanding of the biomechanics and of the 'drivers'. The drivers are the mathematical expression of the relation between two segments. The following text explains the main principles: See a demo here Back to the CONTRIBUTORS'HOMEPAGE
How to contribute as A BIOMECHANIST content media
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Melodicpinpon
Biomechanist
Biomechanist
May 22, 2022
In About the project
Dear Believer, As any evolutionary project, the liberation of knowledge and of the educational medias passes through the three stages: It is first seen as Ridiculous, then it becomes Dangerous, and finally everybody accepts that it was Obvious, since the beginning. The believer sees the success before the others and knows that it is only a matter of time. When a critical mass of believers is reached, the whole society suddenly shifts. Their Faith is the seed from which the future will sprout, grow tall and mighty and finally bloom. Being an early believer is therefore essential, and it deserves a badge. Let's meditate together on the GUERILLA OPEN ACCESS MANIFESTO, Brothers and Sisters. Back to the CONTRIBUTORS'HOMEPAGE
How to contribute as A BELIEVER content media
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Melodicpinpon
Biomechanist
Biomechanist
May 22, 2022
In About the project
Dear Librist, The CC licenses are not only a legal determination, they express an essential vision of the knowledge, the communication, the politics, the economics and the philosophy. Its approach transcends the usual production and exchange processes, allows to produce faster, implies other risks and strategies. The following missions are all meant to connect the atlas to the society: 1) Create a documentation 2) Maintain the website; invite, welcome and support the users. 3) Grow the Community on social medias: Linkedin Facebook Instagram Tiktok 4) create gateways with other platforms: -Wikipedia (Project Anatomy) -Wikimedi.ca -Open Anatomy -Anki -GNU Health -Zenodo -Phenom10K (3D animal's skulls) -Digimorph (Usable animal's skulls slices) -3DSlicer -... 5) Create a theoretical defense of the open source approach compared to the copyright solutions. 6) Communicate with the public institutions, the academic organisms and the public to support the production and the use of open source knowledge. A collaboration with a Graphist could be created for this occasion. Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as A LIBRIST content media
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Melodicpinpon
Biomechanist
Biomechanist
May 21, 2022
In About Blender
Dear Modeler, The purpose of the atlas is to reproduce an accurate model of the human anatomy. Particular techniques are used to meet the needs of a functional 3D atlas of anatomy, but what matters most is the attention to the anatomical dimension. The two essential missions are: -to correct the existing objects following the error reports made by the anatomists -to complete the missing anatomical structures, using the same principles The file weight and RAM needed to display it is essential: If the file is too heavy, it won't run on many devices. Professional anatomists will report the errors that need to be fixed in a spreadsheet. Anatomical books, images, should be used as reference. Many other questions regularly arise; here are the first attempts to explain the particular techniques used in the .blend file. To discuss what to do and share your suggestions and/or contributions, you can answer to this post. The two following subjects also concern the 3D Modelers: Create a FEMALE MODEL Create ANIMAL MODELS Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as A MODELER content media
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Melodicpinpon
Biomechanist
Biomechanist
May 21, 2022
In About Blender
Dear Graphist, An essential function of the .blend version of the Atlas is to export images. These images will be available for free and for all, under CC-BY-SA license and be used to illustrate articles, teach, and learn. When a style has been defined, the renderer is invited to: -export labelled anatomical illustrations (from the verified content) These images are meant to be didactic and aesthetic. -export promotional videos and tutorials are regularly posted on the social medias (Linkedin, Facebook, Instagram, Tiktok, Youtube) Several techniques (montage) can be used or mixed according to the context: Screen capture, Viewport render Animation, Live recording. This option has been used so far as a user-friendly option to export the images: CAMERA SETUP The camera setup of the Atlas allows the camera to be placed using its target object: Press 'Numpad 0' to pass in Camera view Show and Select the object called 'Take a picture' in the outliner Grab it (G), Rotate it (R), Scale it (S) Press F12 to 'Vewport Render Image' (Ctrl+F12 for an Animation) Save your image (F3) VIEWPORT RENDER vs. RENDER The Viewport Renders are faster than the regular Renders. The quality is the same. The regular Render should only be used if you need to use the compositor, or to add special effects like 'Freestyle' (A bunch of line styles are already configured). In this case, all the functions are default, except a very handy button that synchronizes the Render to the Viewport (What you see is what you get) It has to be pressed before each Render in 'N>Z-Anatomy>Visibility>Sync visibility'. To start sharing your renders, you can answer to this post. Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as A GRAPHIST content media
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Melodicpinpon
Biomechanist
Biomechanist
May 21, 2022
In About Blender
Dear Python coder, The 'z-anatomy.py' script, made by Marcin Zielinski allows to use Blender as an atlas of anatomy. It gathers a serie of functions and is run automatically on opening (on Windows) Several things can probably still be done: -Advice the 3D Modelers about the performance -Facilitate the collaboration processes (import, export, merging, ...) -Optimize the existing script, if needed -Export separate add-ons for each functions (for other projects) -Create new amazing functions The best is to download the latest version of the whole .blend file on the 'HOME' page, before working on it, to follow the evolution of the .blend file. To receive or share propositions, you can just answer to this post. Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as A PYTHON CODER content media
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Melodicpinpon
Biomechanist
Biomechanist
May 21, 2022
In About the anatomical content
Hi Translator, 'TA2' or 'TA2-2019' refers to the second edition of the 'Terminologia Anatomica' made in 2019 by the FIPAT. It has been recreated in a Spreadsheet for this project. Automatic translations were generated with 'Google translate'. The green texts have been verified. To correct the translations in black: -either write the correct translation in a comment -or answer to this post to receive an editor access. N.B.1: Compare the TA1 to the TA2 whenever you can; most of the terms remain identical. https://taviewer.openanatomy.org/ https://ta2viewer.openanatomy.org/ N.B.2: Each cell of a column should be unique; the duplicates are highlighted in blue N.B.3: The names in Blender are limited to 61 bytes (//characters), the cells highlighted in pink should be reduced using abbreviations N.B.4: TA1 in Italian, Spanish/Japonese Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as a TRANSLATOR content media
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Melodicpinpon
Biomechanist
Biomechanist
May 21, 2022
In About the anatomical content
Dear Redactor, The atlas automatically displays the definitions of the last selected object. Most of them are a direct copy of the Wikipedia's page. These pages are often very long, and should be summarized. The anatomical structures are often described under another name, or inside the page of another definitions. In order to work in the atlas, these content need to be renamed according to the last version of the 'Terminologia Anatomica' (TA2-2019). This column 'C' of this sheet is set to green if the definition is in the atlas. Certain anatomical structures will have to be described using other sources. In order to respect the copyrights, each sentence should be reformulated in an original way. All the definitions are in English, for the moment. To start working on the definitions: 1) Download the Definition sketchbook 2) Open it in Blender 3) Follow the instructions You are invited to answer to this post: -to ask for changes -to post your new or modified definitions Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as A REDACTOR content media
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Melodicpinpon
Biomechanist
Biomechanist
May 21, 2022
In About the anatomical content
Dear Anatomist, To improve the quality of the open source 3D Atlas of Anatomy, you are invited to verify the anatomical content's accuracy and report the errors. The 'Terminologia Anatomica' (TA2-2019) is the lexicon of all the anatomical structures. To report the errors, add a comment in the Spreadsheet : -Select the cell -Right Click>Commentary -or press (Ctrl+Alt+M) These error reports will be used by the 3D modelers to correct the model. Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as AN ANATOMIST content media
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Melodicpinpon
Biomechanist
Biomechanist
May 13, 2022
In About the project
Dear Anatomists and friends, Welcome to those who want to take part in the evolution of the open source 3D atlas of anatomy. Please choose in which way you want to contribute: As an Anatomist As a Biomechanist As a Translator As a Redactor As a 3D Modeler As a Graphist As a Python Coder As a Developer As a Librist As a Believer Special thanks to: -Ton Roosendaal, who created the software 'Blender' -Kousaku Okubo, who created the original model 'BodyParts3D' -Marcin Zielinski, who created the python script 'z-anatomy.py' -Lluis Vinent, who created the application -Ana Teresa Bigio who translated the whole TA2 in Portuguese We are looking forward to collaborating with you !
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Melodicpinpon
Biomechanist
Biomechanist
Apr 20, 2022
In About the app
Dear Developer, The atlas in Blender is limited to the desktop computers because Blender is a software with plenty of functions, buttons and shortcuts and it would not make sense to try to use it with two fingers on a mobile phone. It is also a hack: Blender is hyper flexible by nature, but very few projects pretend to produce an end-user software directly based on its code; it actually worked very well thanks to the python tricks provided by Marcin Zielinski in his script 'z-anatomy.py'. Lluis Vinent created the app shared on the Homepage; it already works on Android>11 mobiles and on Desktop Computers, and uses directly all the content created in Blender. It is more intuitive and designed to be a 3D Anatomy Atlas. As Blender and the modified version of 'BodyParts 3D', the code of the app is shared on GitHub under CC-BY-SA license. Everybody in invited to discuss how to design a better UI. The Unity Developers are invited to improve the code under the same license.
How to contribute as A DEVELOPER content media
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Melodicpinpon
Biomechanist
Biomechanist
Apr 19, 2022
In About Blender
This small text file explains the techniques used in the open source atlas to create, edit, mirror, name, parent the vessels and nerves. With this tutorial and some perseverance, all the anatomists can now contribute directly to the content of the atlas. Their contribution will then be merged in the file shared on this website.
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Melodicpinpon
Biomechanist
Biomechanist
Mar 25, 2022
In About the project
While the app is automatically updated, the .blend file has to be downloaded again to integrate the latest changes/improvements. For example, many definitions have been added this week.
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Melodicpinpon
Biomechanist
Biomechanist
Mar 06, 2022
In About the project
Here are some documentaries that can help putting this project in perspective: The web to come by Tim Berners-Lee (VOSTFR; 16') -The creator of internet about 'what is data?' https://www.youtube.com/watch?v=OM6XIICm_qo The Internet's Own Boy: The Story of Aaron Swartz (VO; 1h43') -About Open source, Creative Commons, Censorship https://www.youtube.com/watch?v=3Q6Fzbgs_Lg Datagueule: 'Privés de savoir ?' (VF; 10') -About the business of knowledge https://www.youtube.com/watch?v=WnxqoP-c0ZE Dirty Biology: 'La mafia scientifique dont vous n'avez jamais entendu parler' (VF; 12') -About the business of knowledge https://www.youtube.com/watch?v=rcgxY__YXEc
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Melodicpinpon
Biomechanist
Biomechanist
Mar 06, 2022
In About the anatomical content
-Bursae -Tendon sheaths -Temporal bone -Cranium sculpt -Key color on cranial nerves -Integrate neuronal tracts
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Melodicpinpon
Biomechanist
Biomechanist
Dec 05, 2021
In About Blender
APP: -Create HYPERTEXT links that automatically link any anatomical structure mentioned inside the definitions to the definition, name(in the list) and 3D object. PYTHON: -Automatic highlight of the existing/missing structures/definitions from the .blend file -Light file with import options for weaker PC's .BLEND: -Freestyle presets (for Regular Render) -Bursae -Tendon sheaths -Temporal bone -Cranium sculpt
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Melodicpinpon
Biomechanist
Biomechanist
Nov 19, 2021
In About Blender
This version corresponds to the >09-05-2022 versions of the file
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Melodicpinpon
Biomechanist
Biomechanist
Aug 21, 2021
In About the anatomical content
(...) Meanwhile I explored a little of the heart anatomy In your model, the right Coronary artery arises from the anterior aortic sinus and the left Coronary from the left posterior aortic sinus The left mains stem lies between the left auricle and pulomonary trunk In Your model it looks like left main lies drilling through the left auricle The right coronary should arise from the anterior aortic sinus (Location of mouse pointer)
From LinkedIn content media
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Melodicpinpon
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