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Biochemical visualization using Blender

46
By on Video

Mike Pan works on bio-molecular visualization - a strange and mesmerising world.

Mike writes:

Here at the Scientific Visualization Unit of the National Research Council in Pisa, Italy, we have been using Blender since 2008 for doing some very interesting bio-molecular visualization at the sub-cellular level. I myself joined the team just over 3 months ago, and am eager to share some of our work with the Blender community [...]

We use Blender to visualize protein motions and interactions, as well as making short animations that show the inside of a cell in a way that had never been seen with the unaided eye. Because one key focus of the project is scientific accuracy, a lot of time is spent to ensure that the visualization is not only nice-looking, but also scientifically accurate.

Link

About the Author

Avatar image for Bart Veldhuizen
Bart Veldhuizen

I have a LONG history with Blender - I wrote some of the earliest Blender tutorials, worked for Not a Number and helped run the crowdfunding campaign that open sourced Blender (the first one on the internet!). I founded BlenderNation in 2006 and have been editing it every single day since then ;-) I also run the Blender Artists forum and I'm Head of Community at Sketchfab.

46 Comments

  1. dfelinto on

    This is a pretty interesting project. The original post has more details - it's worthy checking. Indeed the Blender Game Engine framework is quite neat.

    Congratulations to all the original team for the project (and for the video). And for Mike Pan for joining the boat and boosting the project with all his multiple abilities. Looking forward to see the final results Mike.

    It's also pretty exciting to see Blender 2.50 being used for that. Who needs a Beta release anyways ;)

    Reply
  2. melon on

    So nice!

    I like all renders very much, but the whole project looks a bit unfinished:

    Some crits (I hope you'll find that constructive):

    - narrator, that explains what is going on would be VERY handy, because a lot of complicated scientific stuff happens,
    - all titles could look better, another font perhaps? Also some additional on-screen text would be nice, during longer sequences
    - music a bit distracting, I would choose some more calm "background" music;

    I've been making medical vis some time ago, I know it's not easy to make it right, so again: good work! Congratulations!

    Reply
  7. kram2301 on

    Great :D
    Looked really nice :)

    I just wish, I knew what goes on / where exactly inside a cell I am at certain parts...

    However, based on the beginning and the end it seemed like a cell that's just about to split into two... So those long strings probably where DNAish stuff, right?

    Reply
  10. Alex DS on

    @Bart : yeah, but i`m a bit disappointed that he couldn't achieve the final project without using others.
    I dream for a day when you don't need other software but Blender. But what do I know, I'm just a beginner in using Blender, just started a few days ago, now I watch tutorials and do little exercises, hope i can manage it 'till the end of summer holiday :D

    Reply
  13. TiZeta on

    @Alex DS: actually, everything that was possibly made with Blender has been made with Blender. Scientific calculation, as for example protein molecular calculation, electrostatic potential and molecular lipophilic potential, can't be done in Blender.
    For what concerns the use of another famous 3d software in the video, that (minor) part have been done a couple of years ago, when we had not switched to Blender yet. Throwing it away didn't make sense for us, as it took a long time to the artist who made it.

    Reply
  15. Ilallegra on

    Hi kram2301!

    I'm really happy you enjoyed the video and you recognized the trip through the cell, but in the movie we never pass the nucleus membrane, so that "long strings" are not DNA filaments but are "tubulin intermediate filaments", that are a sort of polymers having structural features outside the nucleus of the cell and maintain the cell shape and help cell division.

    Reply
  16. Stefano on

    @melon:

    - you're right, considering this video is for general audience,a narrator would help.

    - About the titles, you're right, the titles could have been done better, but these was not the focal point of our efforts. However we will think about this.
    We already have another version of the video with on-screen text, but its not online by now, we have some technical issues, but you will find it online in some days

    http://www.scivis.ifc.cnr.it/

    - And about the music, well, i can understand if you don't like, music is a very subjective matter.
    But, from my point of view, i don't think it is distracting, because the music artist did an very big effort to create
    a sort of music and sound library, so that each subject that enter the scene has an associated sound, and if you
    have different subjects int the scene the sounds mix together but if you listen carefully you will be able to understand each single element. So if every element (more or less) in our movie has ana associated sound i think this is gonna help to understand when this element is in the scene. Along with the different sounds there is also a melodic track, that i personally like.

    Reply
  17. nobody on

    Can't tell whether the running characters along the string (+/-2:07) are scientifically correct, but it looks funny to me ;)
    Different styles of music are used, from background and accomp. music, but the style where the video is used as MTV-clip should be dropped. I personally expect probably some kind of 'deepspace/-sea'-ish music...

    Reply
  19. teo_cazghir on

    I believe that this is a VERY interesting theme, because we are living some amazing times in terms of DND research. I've read about the artificial self replicating cell, created in the lab, teh first artificial organism ever. This kind of discovery really awaken iamgination and make people curious about this field. It;s similar to the space race back in the day, who inspired so many movies, SF books. Now people are interested in genetic research, because this is the future, and not the far future, but the near future, very soon we are going to see more complex organisms created in the lab. Undestanding how they work, what makes them tick is now a must, a part of popular culture. It;s going to be similar to the advent of the microprocessor.

    Reply
  22. RH2 on

    @teo_cazghir:

    They basically copied and pasted the DNA using a computer automated process.
    Then manually injected the genome into "an emptied cell"

    Not much better than a virus.
    Especially because they had to use the original protein expression mechanisms from the original cell.
    Celebration over their achievements is a bit premature, but yes, the possibilities are quite cool.

    Reply
  23. nobody on

    @mike, the other one is even funnier, if both represent the same thing, in "enrique's"-version they seem to carry their paycheck, since yours are running so fast ;)
    For the record, if I would need scientific-proof, one 'prof' telling the other 'prof' is correct won't do... :)

    Reply
  30. pixnlove on

    The music is annoying and horrible ...
    as for the project... I do not know as it is spoil by this horrible and weird music.
    Why do people have no taste at all.
    How could you spend arranging and compose the scene with this truly disguting and horrible music....

    Reply
  31. NRK on

    Amazing, great job in visualization.

    If you see machinery it's hard to believe it created itself. What an amazing work of God.

    I'm not trying to start a debate, for me seeing stuff like this makes me praise Him, it's my reaction and a testiment to the good art done. keep it up! Go Blender!

    Reply
  33. Old Farseeing Art on

    Fantastic! Well done, well done indeed!

    What amazing opportunities this shows! Blender is a wonderful tool - not just art but anything people can imagine can come true in Blender. And when art and science come together, the result is excellent.

    I have several ideas in my head for 10 years now of using Blender to illustrate the results of scientific endeavours; this just might get me to do one or two of them... several involve how to display collected database of information in a way that is able to extend our vision of what happened in the past to what may happen in the future.

    Keep up the excellent work!!!!

    Reply
  34. Ben Holtzman on

    Very cool! I liked trying to recognize the different cellular organs and the processes they were perfoming. Thank you so much, it was very enjoyable.

    Reply
  35. nobody on

    @NRK, you would be amazed how many people believe in a start with an explosion without ingredients(nothing), and to find ingredients not taking space in the first place. The whole thing is fundamentally very unscientific anyway to claim any start without cause/reason. I am amazed that many of these 'great minds' don't except their internal compiler errors...they must be blind like some man told some time ago...

    Reply
  36. TiZeta on

    @nobody, NRK: I could be one of those who believe that someone or something is making life manifest itself, somehow... but please let's keep religious debate (and harsh comments about other people's mind) out of this thread. There are better places and moments to talk about such things. This is not the right place, really.

    Reply
  38. BackiZ on

    Hey,
    I think it is a good animation. I'm a plant/cell biology student and I recognized the most things. Although, I also expected some text to say what is seen. Especially the walking over the mircotubuli is very well done. Did you calculate the density of the particles?

    Somehow these kind of animations Always have some kind of alien music.. ok it's more appropiate than rock music, but that we don't know everything about the processes in the cell doensn't mean we should make it appear more strange with this kind of music. There is nothing wrong with the music itself.

    Anyway, nice done!

    BackiZ

    Reply
  39. nobody on

    @TiZeta; You make your interpretation my words, don't do that, the fact "you could be one of" is undefined as it is already and it's not harsh to repeat what all programmers know, I wasn't making 'a religious debate', I don't even like the word 'church' as it is. Biology is about (a part of) life, so very on topic. You seem to be referring to debates I won't join. My truth isn't democratic nor the outcome of a debate, it actually has to be the truth, very scientific!

    Reply
  43. Bozo on

    This video reminds me of a certain type of demo-scene demos, which take you an a ride over an abstract polygon landscape.
    I have no idea about the chemical processess I'm looking at, but simply knowing that it is a visualization aimed at scientific accuracy makes it even more impressive ;)

    Reply
  44. pixnlove on

    Ffrank you are quite right,
    The music is actually suitable for this sort of organic animation where you don't quite undestand what is going on kind of weird and unexpected constant motion.
    I am a big fan of Nice Melodie but on this occasion it is indeed quite suitable.
    I have changed my mind... Thanks Ffrank
    As for this animation is indeed high quality and very pro.
    My bad...

    Reply
  45. nobody on

    @Ffrank, the link you gave doesn't add anything... I watched, I thank you for the effort, to me, an outsider on the specific subject, the information seems very primitive, and now I have seen 3 visual different versions of what supposed to be 'the same thing'...
    To explain myself; Bart and TiZeta constrain me to hand you only the riddle;
    If I make a 3D-version of my nephew, count your ways of validating the accuracy.

    Niels

    ps.
    Cinematographic-wise, I like Enrique's version most. And no, not because of the paycheck ;)

    Reply
  46. SciVis on

    WOW!!
    Thanks all for the interest you show and the comments.
    I am the 'director' of the entire project, and I take all the blame for things wrong, while all the work was done by the eccelent people working in the group.

    Now the real isues: Narrator voice.
    In my first intent, this was a work of science and art, in which i wanted to just show the beauty of small machines and processes that happen in the cell. I am a biologist, and always figure things. THe idea of making a movie dates back to my university years ('80s), and only now I have been able to actually realize this dream. When you walk in a forest you do not need to know the names or the story of all plants, flowers, animals, smells or things that happen to enjoy it, do you?
    If we were to tell you that what you see is the first report from the exploration of a distant planet, of which we know nothing, we have just been able to catch these few images...
    would you accept this?

    However, i have received enough request to become convinced: we will add a narrator voice guiding people through, as in a tourist guide. The text is almost done, we only need a good voice (possibily without a strong italian accent)...

    In the meantime, those of you that are brave enough to face a quite techinical (both in biology and in computer graphic terms) report, can check the Explanatory Notes .pdf to be found on our website together with the movies.

    The kinesin family. Kinesins are a family of proteins that step along microtubules (the 'running characters along the string'). We depicted one of the smallest, that run very fast (the hypothesis is that the balance of how long and how many of them are on the tracks, informs the cell about microtubule lenghth and abundance, but it's not yet proven). The most attentive will have noiticed that there are few of them. Other members of the family carry vescicles (cargo) and are much slower: it's not a matter of one prof version vs another prof. :-)

    For Broken_sword: you may be interested to visit the forum, on the Blender site, dedicated to Academics and research
    http://www.blender.org/forum/viewforum.php?f=21&sid=cf3e9d850dbeaf65be69f84771b64893 : please add information about the uses of Blender in your university, and feel free to distribute this info to your colleagues.

    Finally please note that all our material will be made available directly when the work will be published, and in the meantime can be obtained form us on request: just go to our website and send us a mail. Mike is doing an eccelent work of interface and streamlining the process, and will keep the community updated on the progress.

    Thanks again for all your comments, and be sure you'll check the version 3+ (with accompanying voice)

    monica (sorry for th long comment)

    Reply

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