Forum Posts

Melodicpinpon
Translator
Translator
Nov 26, 2022
In About the project
Dear Marcin, @Lluís Vinent and Nico, Dear Alexandre, Dear Marek and Bartosz, This is the official 'Assemblée générale' of the 26/11/2022 starting at 15pm. Alexandre is osteopath, uses Blender and Unreal Engine but does not have much time. Marek and Bartosz Barlowski (father and son) contacted me because they like the project and they want to support it and to get involved; we have had a short informal visio as first contact and it appears that: -They own the domain 'Anatomia.pl' and would like to use it to promote the atlas (it could be the occasion to have a more medical professionals-oriented design). It is obviously their right, but 1:Do you think that it is better to build another website (keeping a close collaboration with ours) or do you think that it is a waste of energy/dispersion? I personally think that the domain is beautiful, that it will split the traffic which is bad; it would give them much agility to make their changes without having to ask, which is much more comfortable for them; creating a website is fun but it also takes much time to get it right; especially if there are several languages and a mobile+ a PC version. -Bartosz is interested in exploring the possibilities in Unreal Engine and Marek to share videos using the atlas on linkedin, here again; the app made by Lluis in Unity is already super advanced and the idea to convert it into a web viewer is clear, but Bartosz also considers using another tool -a kind of advanced sketchfab equivalent- to share reviewed parts of the model on their website. Here again it is obviously their right but it can be good to hear the pros and cons: 2:What are the advantages and disadvantages of using this other tool? In my opinion, it is good as long as there is no web viewer, but I see only advantages to the use of the app made by Lluis if a web viewer is produced. -They are keen to join the association (see status in attachment), 3-Do you accept them to integrate the association as members? I have seen that they are in the same spirit and -for me- they are very welcome to take initiatives and responsibilities as the project has many needs and few resources. -Lluis now has the administrator status to share posts on the linkedin page and a canal only for the app on the Discord page. The Youtube/Instagram/Facebook/Tiktok pages are available to anyone who wants to promote the atlas on it. 4: Does anyone want to use them? 5: Does Marek/Bartosz want to use these accounts? The posts on Linkedin could be posted on the 'Z-Anatomy' page and then the link pasted in our personal pages (that's what I missed on the last one so that the likes do not sum up); the same should be possible with facebook etc.. This would provide freedom and visibility to the creator while driving attention both to its own page and to the one of the project. -It is the occasion to speak about the membership: Inviting and officializing the membership of sympathisers, followers and contributors would help them to feel being part of something, open possibilities about the decision-making (online votes), and open possibilities to try and become an association 'of public utility'/'of general interest'. We would need to ask name, first name, and a signature+ a symbolic 1 euro (I think) and to add the invitation on the website, through a post on the social medias and then in the invitations and all the new contacts that we create. Besides the membership, the process of promoting the contributor could improve much the motivation to participate: 7: What rewarding system or recognition could we offer to make the people want to contribute? 8: Do you want to create a vote on something? I would on the automatic translations and the local hosting of the descriptions. What matters much to me is to involve other people than Lluis and me in the decision-making. Users and contributors with their own real needs. Many sites use badges on their forum, I made some but our forum is quite dead. I think that a special post on the social media featuring the contributor and his contribution should do; I think that it could be good to keep a coherence of tone and visual construction of the posts (see posts). 9: What do you think of it? -The youtube channel will be only dedicated to 'Z-Anatomy'; it is unfortunately linked to my personal email (kervyngauthier@gmail.com), Would we concentrate the posts on this channel? I can compromise to give the address to the association but I still use it regularly so that I would not give all the access to everybody at first. Creating another one would mean losing the >8k views which give some credibility. 10: Where would you like to post your the videos? -The youtube channel has a playlist where I'd like to gather the videos about the open source thema; please let me know if you have good youtube links (only the ones that you really like). I did not improve the .blend since a moment and may have less time if I get a job. I feel that the best I can do for the moment is to try and help welcoming new actors -as Marek and Bartosz- and provide a coordination service to allow all the information to circulate well -as this email tries to do. I am also very open to leave these tasks of coordination to somebody else if anyone feels like so. There are already a bunch of people that I want to invite and that I hesitated to add as recipients of this email. 11: Does any of you want to do it? My only demand about it would then be to communicate quickly and openly, and try to reach a nice democratic efficient system. For all the further communication, I propose to give much priority to the forum; It seems the best way to speak publicly about public matters while Linkedin/Discord/... may be more suited to quick tchat and collaboration (we have used Linkedin with Lluis but I think that he prefers Discord) 11: Do you agree with using the forum for further communication? I'll paste this message in a post to allow you to answer inside it if you are ok with it. Who knows if some day somebody finds a way to create an error-reporting system that could be used directly from the app/webviewer but until then, the list that can be pasted in a post of the forum is very clean and handy to communicate and update a to-do list as the one that has been used for the app. If some contributors of 3D modelers appear, there could be the same for 3D content edition. -I wonder if the letter sent by Lluis with his signature to create the bank account of the organization has not been lost on the way but, when it will be done, I propose to add a button for donation through 'Librapay', and to decide with the members how to spend it (we already have a list of wishes) 12: If it does not arrive; can I fake your signature manually with your benediction or do you prefer to send it again (there is no hurry)? 13: Do you want to propose other income strategy? Hugs, Gauthier
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Melodicpinpon
Translator
Translator
Oct 07, 2022
In About the project
After nearly two years of regular short exchanges on the open source atlas of anatomy with many actors of the Digital Health, it appears that: - A legal & technical thinking and action would be needed to defend 'the Commons': A problematic 'grey zone' appears when open source content gets mixed with proprietary formats or technologies. A CC-BY-SA-NC (Non-Commercial) license seems necessary to prevent the commercial recuperation. - (Really) Free is scarce, open is exceptional, collaborative still has to be invented. Collaborative is defined here as 'Sharing the source files during the development'. - Many people express the will to contribute but nearly no one does; the technical solution to collaborate (google spreadsheet, forum, Linkedin community) need to be improved/developed. Could a pro-active support of the people who express the will to contribute change the situation? Who would do it? - 'Z-Anatomy' shares copies of Wikipedia's pages as description of most anatomical structures and automatic translations of it. There are two different ways to develop this part: -A Database -Links to Wikipedia/data A combination of both would help to avoid the obstacles of the wiki edition process, while creating links with it. Direct connections from and to the Wikipedia/data/commons (a link at the bottom of the wikipedia's page would open the atlas centered on the corresponding structure) could provide more traffic (when the new web viewer will be available) and allow everyone to contribute in the right place: definitions/descriptions of the anatomical structures in the wikis, and 3d representation and organization in the atlas; while a database would make it much easier to edit the content and let the users become editors. (There are about 7000 anatomical structures and English, French, Spanish and Portuguese) The following message will be sent to the academic organisms that are/plan to/will work using the files shared on this website: I know that your time is precious and I will therefore be synthetic: I am writing this email to you for different reasons: 1. We are all active and actors in the field of 3D modeling, in particular in the field of anatomy. For this reason, I want to create - in the case of a shared interest in participation - a platform for discussion between us. It seems to me that exchanges could be useful to us, for the quality and efficiency of our work at all. In the event of a positive response and if necessary/desired, we can put the idea of ​​an exchange space in place on any other device than an exchange of emails. 2. I would like to ask – in a direct way, I admit it and ask you in advance to understand me – which of you is interested in the idea/principle of some form of collaboration in our work? , which after all have the same vocation: the use, improvement and sharing of the '3D Atlas'? 3. Is there agreement in principle that a coordinated improvement of the content of the atlas is more efficient and therefore more useful to everyone (including the public) and that it would therefore be preferable to to have - as far as possible and according to methods to be defined and improved if necessary - a coordinated and integrated management of future developments? 4. The previous points seem to me the most crucial. Nevertheless, I add this: in the event of a positive response to the previous points: who would be open to sharing digital material, ideas, subsidies, or any other useful element?More generally, who feels interested in the idea of further collaboration in the future? The message became a post to make it easier to get back to it in the future but can be considered and answered to as a personal email.
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Melodicpinpon
Translator
Translator
May 26, 2022
In About the project
The users who can not use the .blend because of the RAM needed to open the file can now right click on 'Z-Anatomy-lite.blend' (at the end of the 'Anatomy Blender' folder) and open it inside the same portable version. The main collections -corresponding to the main systems of the body- can now be linked very easily inside this empty file clicking on the buttons with their name (see image). This option only works for Windows for the moment but there is probably a way to use it on Mac and Linux.
LIGHT VERSION content media
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Melodicpinpon
Translator
Translator
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
Translator
Translator
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, the best option would probably be to have: 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. Alternatively, it would be possible to adapt the shapes of the male model to other references -without using a .dicom (it would actually be easier). 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
Translator
Translator
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 'Atlas' page of this website, beneath the App. 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
Translator
Translator
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
Translator
Translator
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
Translator
Translator
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
Translator
Translator
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
Translator
Translator
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. https://github.com/theres1/Z-Anatomy-app-template Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as A PYTHON CODER content media
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Melodicpinpon
Translator
Translator
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 ---- For the vertebrate domesticated animals (Cats, Dogs, Horses, Bulls, Sheeps, Goats, Pigs, Rabbits, ...), the anatomists use the 'Nomenclatura anatomica Veterinaria'(NAV), created and shared as a .pdf by the 'World Association of Veterinary Anatomists'(WAVA). It needs some love; great open source models can be realized with your help. Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as a TRANSLATOR content media
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Melodicpinpon
Translator
Translator
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
Translator
Translator
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. Cell A in red means that the anatomical structure is represented as a label in the atlas Cell B in purple means that it is represented as a 3D object Cell C in green means that the structure is linked to a definition Cell D in color indicates that the structure has been verified by somebody The people willing to verify the anatomical accuracy of a part of the lexicon can ask for an editor's access to the spreadsheet. When it is done, please choose your own color, and start verifying if the structure of the list is well represented in the atlas; if it is right, pass the cell of the column D in your color. If there is something to modify, pass it to another color (redish) and describe the error in a few words in a commentary (RMB>Comment). When a modeler has fixed the error (or a serie), he can ask the anatomist to re-check and pass it to 'correct'. (or pass it to yellow 'please re-check' color) Back to the CONTRIBUTOR'S HOMEPAGE
How to contribute as AN ANATOMIST content media
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Melodicpinpon
Translator
Translator
May 13, 2022
In About the project
You are invited to take part in the development of the atlas: 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 We are looking forward to collaborating with you ! 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 -Carlos Torres Villar who translated the whole TA2 in Spanish
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Melodicpinpon
Translator
Translator
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. Edit (october 2022): The source code of the evolving new DesktopWin10-application is here. 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. Back to the CONTRIBUTORS' HOMEPAGE
How to contribute as A DEVELOPER content media
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Melodicpinpon
Translator
Translator
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
Translator
Translator
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
Translator
Translator
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
Translator
Translator
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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