5 Time-lapse Videos, from Very Small to Very Big

"Slow" marine animals show their secret life under high magnification. Corals and sponges build coral reefs and play crucial roles in the biosphere, yet we know almost nothing about their daily lives. These animals are actually very mobile creatures, however their motion is only detectable at different time scales compared to ours and requires time lapses to be seen. Make sure you watch it on a large screen! You won't be able to appreciate this clip or see individual cells moving in a sponge on a smartphone. This clip is displayed in Full HD, yet the source footage (or the whole clip), is available in UltraHD 4k resolution for media productions. Visit my website to see more work: www.microworldsphotography.com Learn more about what you see in this video: http://notes-from-dreamworlds.blogspot.com.au/2014/03/slow-life.html The answer to a common question: yes, colors are "real" and not exaggerated by digital enhancement. I have only applied basic white balance correction. When photographers use white light on corals, they simply miss the vast majority of colors. Read more about fluorescence and why these corals are natural: http://notes-from-dreamworlds.blogspot.com.au/2013/06/fluorescent-colors-of-reef-coral.html The duration of sequences varied from 20 minutes to 6+ hours. === Technical details === To make this little clip I took 150000 shots. Why so many? Because macro photography involves shallow depth of field. To extend it, I used focus stacking. Each frame of the video is actually a stack that consists of 3-12 shots where in-focus areas are merged. Just the intro and last scene are regular real-time footage. One frame required about 10 minutes of processing time (raw conversion + stacking). Unfortunately, the success rate was very low due to copious technical challenges and I spent almost 9 long months just to learn how to make these kinds of videos and understand how to work with these delicate creatures. I am glad that I abandoned the idea of making this clip in 3D (with two cameras) - very few people have 3D screens and it doubles processing time. Gear: - Cameras: Canon 7D (died at the beginning of the project as I had overused it in my research), Canon 5d Mkiii (90% of footage is done with it) - Lenses: Canon MP-E 65 mm lens, and a custom photomacrography rig (custom lenses are better for this type of task) - Lights: adjustable custom-spectrum lamps (3 different models) - they were needed to recreate natural underwater illumination. - several motorized stages, including StackShot for focus stacking. StackShot, is sadly not 100% reliable at all and kept destroying my footage. - multiple computers to process thousands of 22+ Mpx raw images and perform focus stacking (an old laptop died on that mission after 3 weeks of continuous processing). Edited in Sony Vegas, Adobe Photoshop CS6, Zerene Stacker, and Helicon Focus. Music: Atmostra III by Cedric Baravaglio, Jonathan Ochmann and Zdravko Djordjevic. === Sharing/Use === Inquiries/licensing/press: find my contact details here: http://www.microworldsphotography.com/About Please do not share this clip to promote or endorse marine aquarium industry. I simply want people to admire life, but not to be told to buy stuff, especially poses captive animals More about using my videos: http://www.microworldsphotography.com/Image-Use/Video-Use-and-Licensing (consideration to buy a print from my website or to use the tip jar below the video is always welcome, but this option is better: https://secure.marineconservation.org.au/donate.php?campid=701900000006kqX)

Above: Slow Life by Daniel Stoupin.

After 9 months and 50,000 shots (only using 5.000 for the final video), my first flowers timelapse has finished. After a long work looking for flowers that would open fast, here is a list of the flowers that have been part of the timelapse: Lillium, hibiscus, carnations, orchids, dandelions, lilies, daisies, alstroemeria, peonies and nigella damask. Here is my web: http://www.daviddelossan.com You can follow me on twitter: https://twitter.com/DaviddelosSan If you want to license any of my images or videos, contact me at david4112@hotmail.com Music of Roger Subirana - Point of no return ------------------------ Después de 9 meses y 50.000 fotografías (de las cuales solo han formado parte del vídeo final unas 5.000), mi primer timelapse de flores ha terminado de formarse. Tras un largo trabajo buscando flores que abriesen rápido, aquí esta la lista de flores que han formado parte del timelapse: Lillium, hibiscus, clavelinas, orquídeas, dientes de león, lirios, margaritas, alstroemerias, peonías y nigella de damasco. Aquí tenéis mi web: http://www.daviddelossan.com Podéis seguirme en twitter: https://twitter.com/DaviddelosSan

Above: Flowers Opening Timelapse by David de los Santos Gil.

https://www.facebook.com/LightalivePhotography http://www.lightalivephotography.com/ Song - "Leader" by MODE https://www.facebook.com/M0DE0 https://itunes.apple.com/us/artist/mode/id923642693 http://electriccomposer.com/ https://soundcloud.com/dannyodom The first Stormscapes here (may ease you into the second one): https://vimeo.com/86112567 High plains storms are some of the most beautiful and wild in the world. I spent May - September 2014 photographing all types of severe weather in Wyoming, Montana, South Dakota, Nebraska, and Colorado. This time lapse project is a result of that effort. From rainbows to tornadoes, there is a little bit of everything in here. Copyright Nicolaus Wegner/lightALIVE Photography. Please message or email for inquiries regarding pricing. A word on embedding. I generally have no problems with this, have at it (I gladly encourage social media sharing!). Broadcasting is out as it is against the music licensing agreement. Individual sequences from video (and more) are available for licensing, or you can hire me to put a video together, but no freebies. This video will not be uploaded anywhere other than Vimeo. Please do not ask. Gear: Canon 5dm2 and 6d 16-35m2 14mm Rokinon 70-200 f4L tripods and remotes a few spare pairs of clean underwear Edited in Lightroom and After Effects

Above: Stormscapes 2 by Nicolaus Wegner.

Time lapse sequences of photographs taken by the crew of expeditions 28 & 29 onboard the International Space Station from August to October, 2011, who to my knowledge shot these pictures at an altitude of around 350 km. All credit goes to them. Full HD, refurbished, smoothed, retimed, denoised, deflickered, cut, etc. All in all I tried to keep the looks of the material as original as possible, avoided adjusting the colors and the like, since in my opinion the original footage itself already has an almost surreal and aestethical visual nature. Music: Jan Jelinek | Do Dekor, faitiche back2001 w+p by Jan Jelinek, published by scape Publishing / Universal http://www.janjelinek.com | http://www.faitiche.de Image Courtesy of the Image Science & Analysis Laboratory, NASA Johnson Space Center, The Gateway to Astronaut Photography of Earth http://eol.jsc.nasa.gov Editing: Michael König | http://www.koenigm.com Shooting locations in order of appearance: 1. Aurora Borealis Pass over the United States at Night 2. Aurora Borealis and eastern United States at Night 3. Aurora Australis from Madagascar to southwest of Australia 4. Aurora Australis south of Australia 5. Northwest coast of United States to Central South America at Night 6. Aurora Australis from the Southern to the Northern Pacific Ocean 7. Halfway around the World 8. Night Pass over Central Africa and the Middle East 9. Evening Pass over the Sahara Desert and the Middle East 10. Pass over Canada and Central United States at Night 11. Pass over Southern California to Hudson Bay 12. Islands in the Philippine Sea at Night 13. Pass over Eastern Asia to Philippine Sea and Guam 14. Views of the Mideast at Night 15. Night Pass over Mediterranean Sea 16. Aurora Borealis and the United States at Night 17. Aurora Australis over Indian Ocean 18. Eastern Europe to Southeastern Asia at Night

Above: Earth by Michael König.

Edited time lapse sequences of the sun’s atmosphere observed by the Solar Dynamics Observatory spacecraft between 2011 and 2015. Music: Una by Murcof Taken form the Album Utopía (2004) | CD: BAY 38CD, Digital: BAY 38E http://www.theleaflabel.com/en/releases/view/98/murcof/utopia Images courtesy of: NASA's Goddard Space Flight Center, Scientific Visualization Studio www.nasa.gov/centers/goddard | http://sdo.gsfc.nasa.gov Editing: Michael König | http://www.koenigm.com Additionally EARTH is now provided in Full HD: https://vimeo.com/32001208 This montage features excerpts of 4K full-disk pictures in extreme ultraviolet channels, mainly using wavelengths of 30.4 nm (50,000 Kelvin) partially in combination with 17.1 nm (6.3×105 Kelvin), and offers a glance at spicules, solar flares, filaments and an overview of the sun’s atmosphere. The footage was captured by the Atmospheric Imaging Assembly (AIA) maintained by the Joint Science Operations Center (Lockheed Martin Solar and Astrophysics Laboratory in collaboration with Stanford University) Scenes in order of appearance: 1. Long shots of solar activity | October 2013 2. Boiling solar prominence | February 2013 3. Close up active regions | October 2013 4. Launching filament | November 2011 5. Twisting prominence | September 2012 6. Close up solar activity | October 2014 7. Solar prominence | July 2013 8. Lunar transit | January 2014 9. Solar prominence dance | December 2012 10. Solar activity | October 2013 11. Plasma eruption | September 2012 12. Coronal rain | July 2012 13. Close up active regions | October 2013 14. Trebuchet eruption | February 2011 15. Solar prominence | October 2013 16. Venus transit | June 2012 17. Extreme solar eruption | June 2011 18. Filament eruption & ’canyon of fire’ | September 2013 19. Erupting solar filament | March 2015 20. Comet ’lovejoy’ passes sun | December 2011 21. Earth eclipse and dark prominence | September 2012 More information on the Solar Dynamics Observatory mission: http://en.wikipedia.org/wiki/Solar_Dynamics_Observatory

Above: Sun by Michael König.

Irving Geis and His Paintings of Proteins

“Crystal structure of myoglobin (1961)” from the Irving Geis Collection. Rights owned and administered by the Howard Hughes Medical Institute. Reproduction by permission only.

The image above was a painting of myoglobin, the first protein structure solved by X-ray crystallography. The painting was created by Irving Geis for a Scientific American article “The Three Dimensional Structure of a Protein Molecule” by John Kendrew, published in December l961. John Kendrew and his colleagues solved the myoglobin structure in l958.

Irving Geis (1908-1997). Photo: Sandy Geis.

Nowadays, one can easily create an image of a protein structure with the aid of a computer and molecular visualization software. In 1961, however, everything had to be done by hand. Creating an image of a protein structure required not only outstanding artistic skills of visualizing complicated 3D structures, but also extraordinary patience. Originally trained as an architect at Georgia Institute of Technology and receiving a Bachelor of Fine Arts from University of Pennsylvania, Geis had all the skills and knowledge to visualize the 3D structures of proteins.

Geis created this painting by first photographing the physical models and then by creating voluminous sketches and studies before painting the finished version [1]. A lot of refinements were made during the sketch step based on the feedback from John Kendrew, as shown by the image below. The final painting took 6 months to complete [2].

“A draft image of the 1961 myoglobin” from the Irving Geis Collection. Comments on the image were made by Irving Geis and John Kendrew. Rights owned and administered by the Howard Hughes Medical Institute. Reproduction by permission only.

I tried to mimic Geis’ myoglobin image by using UCSF Chimera and Maxon Cinema 4D. It took me quite some time but the result is far inferior to the original masterpiece. The heme group seems OK, but the alpha helices are hard to recognize even though I used the same color scheme as Geis’ painting, depth cueing effect, and some lighting techniques in Cinema 4D. In addition, I couldn’t add hydrogen atoms except those in hydrogen bonds in my version, as the model would become overwhelmingly complicated to be meaningful at all. On the other hand, Geis’s painting clearly visualizes the main structural features (the heme group and alpha helices) while giving an overall sense of the structural complexity of the myoglobin protein.

My attempt to mimic Geis’ painting using UCSF Chimera and Maxon Cinema 4D (PDB ID: 1MBN). The alpha helices are difficult to recognize because they overlap with the atoms in the back.

To achieve this, Geis used a process he called “selected lying” [2-4], in which he made small adjustments to avoid structural overlapping. He might distort the protein a little bit here and there, or he might use slightly different viewing angles or perspectives for different parts of the protein. In the end, this process resulted in a structure that was not so different from the real structure, but much easier to understand on a flat paper. A computer, on the other hand, draws everything based on the given coordinates and the image it produces is usually not very comprehensible, especially for complicated protein structures.

“Crystal structure of lysozyme (1966)” from the Irving Geis Collection. Rights owned and administered by the Howard Hughes Medical Institute. Reproduction by permission only.

Besides his excellence in visualizing complicated 3D structures, what makes Geis’ paintings special is his belief that “his job was not to draw a protein exactly as it was, but to show how it worked”[3]. Often Geis would add additional layers of information on top of protein structures, making protein functions and mechanisms understandable. This is the reason why his protein paintings are still appreciated and used in some textbooks, even today.

Colors are very important to Geis’ painting. He carefully chose the proper colors to illustrate the inner workings of proteins. “Color is a language”, he said, “and as with any other language, one mustn’t babble!” [3]

“Cytochrome C (1989)” from the Irving Geis Collection. Rights owned and administered by the Howard Hughes Medical Institute. Reproduction by permission only.

Geis had worked with many scientists in his career. Among them, Dr. Richard Dickerson was his long time collaborator and friend. The two co-authored several books, including The Structure and Action of Proteins (1969), Hemoglobin (1983), and a chemistry textbook: Chemistry, Matter and the Universe (1976). The Structure and Action of Proteins became classic after published and inspired a generation of young biochemists.

Irving Geis was born in 1908 in New York City and died in 1997. He was 88 and lived in Manhattan.

“Irving Geis and his work-in-progress 1961 myoglobin painting” from the Irving Geis Collection. Rights owned and administered by the Howard Hughes Medical Institute. Reproduction by permission only.

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Interview with Dr. Richard E. Dickerson about Mr. Geis

1. It’s rare that an artist shares the authorship with a text writer. However, you and Mr. Geis coauthored 3 books together [The Structure and Action of Proteins (1969), Chemistry, Matter and the Universe (1976), Hemoglobin (1983)]. As you wrote, “I could describe what needed to be illustrated about protein structure, and Irv would come up with clever and original graphic methods of putting the point across. It was never clear whether Irv illustrated my books, or I wrote Irv’s captions.”[3] Could you please share with us how Mr. Geis was able to get such a deep understanding of proteins?

It is my understanding that he acquired his background knowledge slowly by illustrating for magazines such as Scientific American.  Indeed, it was his illustrations for John Kendrew’s myoglobin structure that first caused us to meet in New York in 1963.  He was a very intelligent man, and simply read a lot about scientific matters in order to make his diagrams more meaningful.

2. In you books, I am really amazed that Mr. Geis was able to depict sophisticated protein structures and functions with only black/gray and another color. The images are not only easy to understand but also elegant. Could you please comment on this?

Irving Geis was a true artist.  A skillful artist can convey information that a simple draftsman cannot.  His use of color and shading for emphasis was masterful. 

3. As you wrote, Mr. Geis used a process he called “Selective Lying” to tweak the protein representation if “some key aspect of protein structure was eclipsed and out of sight”.[3] The end result is a protein structure and its molecular mechanism easy to understand. Personally, I am firm believer of this approach. But others might think we should not alter the structure at all. What is your opinion on this?

The purpose of Irv’s scientific drawings was to convey information about how the molecules work, and not simply to illustrate the fine-structure details of the molecules.  For the latter, one should turn to the Protein Data Bank (PDB) or other such archives.  If a certain amount of artistic licence would aid the reader in understanding how the molecule worked, then such behaviour is not only legitimate; it is constructive.

4. As our knowledge of protein structure and function grow rapidly, computer animation becomes a common media to depict the dynamic protein behaviours in the cell. Compared with traditional protein illustrations, what are the pros and cons of computer animations? What would be the basic requirements for artists/scientists creating these animations?

I have no strong opinions on this.  If computer animation is available to a research worker or a student, then it obviously could assist him in understanding the macromolecule.

5. You mentioned in an article[5] that you regretted you were not able to write Atlas of Protein Structure with Mr. Geis at a time when there were only 8 protein structures. Nowadays, we have nearly 100 thousands protein structures in the Protein Data Bank. Do you think it is still necessary write a new Atlas to give students and hopefully the general public a feel of the richness and magic of protein structures? If you do, how many proteins should be included in this challenging book?

I think that the days of an atlas that contains every known structure are over.  No one can write a book that discusses 100,000 different protein structures.  The PDB is a resource that allows people interested in a certain class of protein to learn how many such proteins have been solved and what each of them looks like.  It is true that one could write a general book on protein structure/function relationships, and indeed some have done so.  Such authors would select those of the 100,000 different structures that pertained to the matter at hand, or a set of structures that gave a general impression of protein structure.  But to discuss all 100,000 structures individually:  No.

6. Finally, what is your favorite illustration(s) of Mr. Geis and why?

I simply could not come up with one particular “favorite” illustration; Irv has done so much and done it so well.  I like his haemoglobin/myoglobin and his DNA illustrations, because these concern subjects in which I had a scientific relationship.  But someone else would undoubtedly give you a different list. 

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Acknowledgement

I would like to thank Sandy Geis for reviewing this article and generously providing many reference materials about Mr. Geis’s works. I would also like to thank Howard Hughes Medical Institute for granting permissions to use the above images from the Irving Geis Collection. Finally, I am grateful that Dr. Dickerson took the time to answer my questions.

Rreferences

[1] S. de Chadarevian, Models and the Making of Molecular Biology, in Models: The Third Demension of Science (eds. S. de Chadarevian and N. Hopwood) 339-368 (Stanford Univeristy Press, Stanford, California, USA, 2004)

[2] B. P. Gaber and D. S. Goodsell, Irving Geis: Dean of Molecular Illustration. Journal of Molecular Graphics and Modeling 15, 57-59 (1997)

[3] R. E. Dickerson, Irving Geis, Molecular artist, 1908-1997. Protein Science 6, 2483-2484 (1997)

[4] D. S. Goodsell and G. T. Johnson, Filling in the Gaps: Artistic License in Education and Outreach. PLoS Biology 5, 2759-2762 (2007)

[5] R. E. Dickerson, Obituary: Irving Geis, 1908-1997. Structure 5, 1247-1249 (1997).