tag:blogger.com,1999:blog-1970123582882990422024-03-19T00:56:53.723-04:00BiocinematicsStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.comBlogger320125tag:blogger.com,1999:blog-197012358288299042.post-76633703134410405052019-02-26T16:13:00.000-05:002019-02-26T16:13:28.010-05:0010th AnniversaryTen years ago today I wrote a short blog post entitled "<a href="https://biocinematics.blogspot.com/2009/02/blog.html">Blog?</a>". It was the first post on this blog, and the public beginning for Biocinematics. For the 10th anniversary of this blog, I'd like to reflect on the past decade of work by presenting my 2019 Demo Reel:<br />
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<iframe allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/v3Xg6-09uaE" width="640"></iframe>
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I wasn't able to include any of my work from AXS Studio, so there aren't as many new pieces to share as I'd like, however this upcoming year is about creating fun new projects.<br />
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Speaking of looking forward, as I mentioned in my previous post, this will be the last post I write on this blog. In the future I will be writing posts on my website: <a href="https://www.biocinematics.com/" target="_blank">www.biocinematics.com</a><br />
Why the transition?<br />
<br />
<ol>
<li>The Squarespace platform will hopefully allow me more flexibility to construct my blog as I desire, and (importantly!) provide a better mobile reading experience.</li>
<li>It will allow me to have tighter integration with the rest of my website and have more things in one place.</li>
<li>As I've written before, I am entering a new period of my career, and I'd like to focus on what's ahead with something of a clean page or fresh beginning.</li>
<li>10 years is a nice round lifespan for a blog, don't you think?</li>
</ol>
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Will I migrate all my existing posts to the new blog? No, these posts are a good archive, with lots of links pointing to them, and I'd like to leave those alive and in-place. Looking back, most of my early posts were about learning the tools I'd need to start making science animations, and there's a lot of stuff which is almost embarrassing, but I don't think it's wise to purge them. In fact, I went back to try to find the first original 3D model I created. I can't access any of the Maya "Personal Learning Edition" or Anim8or models I made when I was dabbling in 3D c.2003-2005, but I did come across this incomplete model of a radio I made on April 04, 2009.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1HI3bJNxEJ7qy4rw9ADEtLZyB85mKPwRYb3fhyphenhyphen-GY_29INa5g3_iiLyWwBofCuB94MUzpk8rtR4q-UdcBgN_dgEu9W3kCIVglopFlH4Ql6mD-_9wgNdmNmkU8qOR7dHmMkCTkNsUUuKZw/s1600/Radio_game_asset_2009Apr04_cropped.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="876" data-original-width="546" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1HI3bJNxEJ7qy4rw9ADEtLZyB85mKPwRYb3fhyphenhyphen-GY_29INa5g3_iiLyWwBofCuB94MUzpk8rtR4q-UdcBgN_dgEu9W3kCIVglopFlH4Ql6mD-_9wgNdmNmkU8qOR7dHmMkCTkNsUUuKZw/s400/Radio_game_asset_2009Apr04_cropped.jpg" width="248" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Clearly I was going to mirror it... look only at the right side.</td></tr>
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I think I was trying to make game assets for a concept my brother had come up with. I guess I've improved since then. I'm excited to see where the next decade will take me, and I hope you'll come along for the journey, or at least stop by periodically.<br />
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Thanks for reading,<br />
Stuart<br />
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P.S. Call to action: If you like the kinds of science animations I have in my demo reel, please consider "liking", sharing, and/or commenting on the <a href="https://www.youtube.com/watch?v=v3Xg6-09uaE" target="_blank">YouTube video</a>. It does help improve the visibility of my work. Thank you!Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-922199542384165032019-02-22T16:30:00.000-05:002019-02-22T16:30:51.484-05:00Ripping threads: a new workstation Before we get started, if you'd rather see the super short version with mostly just pictures, <a href="https://instagram.com/biocinematics/" target="_blank">check out my Instagram profile</a> instead. Okay, on with the post. I recently purchased and assembled a new PC! Reason 1: My previous home workstation was purchased <a href="https://biocinematics.blogspot.com/2009/09/stop-harpin-on-new-computer.html">a little over 9 years ago</a>. Reason 2: I'll be making computer animations that are fairly demanding with respect to computer hardware.<br />
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Yes, it was past time for me to build a new computer. Over the years, I have made some additions and replacements here and there to my old machine; I chronicled one such upgrade in this tongue-in-cheek <a href="https://biocinematics.blogspot.com/2010/05/changing-hard-drive.html">blog post</a>. However the core of my old computer has been a constant and stalwart workhorse and has enabled me to <a href="https://biocinematics.blogspot.com/2011/01/demo-reel.html">apply to</a>, <a href="https://biocinematics.blogspot.com/2013/07/recording-illuminated-neuron-final.html">complete</a>, and <a href="https://biocinematics.blogspot.com/2019/02/knots-and-robots.html">make use of</a> a Master's of Science in Biomedical Communication. It's a bittersweet parting.<br />
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Part of the reason (beyond the expense) it took so long to upgrade is because purchasing a computer comes with so many decisions: <b>Windows</b>, Mac, or Linux? Laptop or <b>desktop</b>? Pre-assembled or <b>self-assembled</b>? Intel or <b>AMD</b>? <b>NVidia </b>or AMD? Water-cooled or <b>air-cooled</b>? How <b>much </b>RAM? Everything fits in the case, <b>yes</b>? How about that Samsung NVMe boot drive: Pro or <b>Evo</b>? And do you really need a USB type C port on the front of the case? <b>No</b>, but calculus involving shipping times, availability, cost, colors, side panels, so <b>yes </b>I have one. The list is nigh endless.<br />
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I'm not going to discuss pros and cons or rationalize all the decisions I made. I am confident that I did sufficient research and made decisions that were right for me, which are not going to be the choices that anyone else should necessarily make. I try hard not to be a fanboy for any company (I'll admit my chief failing in this regard is Redshift3D). I don't think brand loyalty is worth very much for <i>consumers</i> of hardware, though it's worth a tremendous amount for <i>companies</i>. Food for thought.<br />
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So <span style="font-size: x-small;">(five paragraphs in)</span>, let's cut to the good stuff. All the components arrived in exciting boxes. The case shipped later, so I opted to assemble the guts outside the case in the meantime to make sure I didn't have any dead components.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhY4bWwiPKsTZh03wPNQEtNCnyhO4zlkVYjTpsdAO0ShvQd2mI-FW-tKDIuCqaYHwUlN-dUkApg5wj5zYWrluTI30pYWJ8CyHKi8u6LOjgBDXFwtMQOAYI5kNsG7eEn62ZvzYh1F-U9TQQ_/s1600/SJantzen-20190112_11610.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhY4bWwiPKsTZh03wPNQEtNCnyhO4zlkVYjTpsdAO0ShvQd2mI-FW-tKDIuCqaYHwUlN-dUkApg5wj5zYWrluTI30pYWJ8CyHKi8u6LOjgBDXFwtMQOAYI5kNsG7eEn62ZvzYh1F-U9TQQ_/s640/SJantzen-20190112_11610.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Like Christmas morning</td></tr>
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I cleared off my desk (it's never this tidy), stole my wife's MacBook for on-the-fly support and troubleshooting, and grabbed my iFixit toolkit (a worthwhile birthday splurge).<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1alrtBJFAcJqiNQbV9-VbXXgR4L8ra3tBVMrhZrt9ZAk0Oeicanic4hhDZQjwsDg_2zdC05Q0bAtoA-A5cDXYfLRdE4L1OtAJR_hO69nYxwFwkqe45qf116UaTaCzssNj6wvDwdbDqyJt/s1600/SJantzen-20190112_11606.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="607" data-original-width="1080" height="358" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1alrtBJFAcJqiNQbV9-VbXXgR4L8ra3tBVMrhZrt9ZAk0Oeicanic4hhDZQjwsDg_2zdC05Q0bAtoA-A5cDXYfLRdE4L1OtAJR_hO69nYxwFwkqe45qf116UaTaCzssNj6wvDwdbDqyJt/s640/SJantzen-20190112_11606.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The streetcar print was a secret santa gift. I love it/hate it.</td></tr>
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I grounded myself with an anti-static wrist strap (not pictured) and placed the ROG Strix x399-E motherboard on its box to use as a non-zapping workbench.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjh2J5mHDMB7503fo0Y5FhN57wsMmHYffYAAlBzJH3cm_2QGPzZk8ph07wmVvcVvpnP38l29-pP8I1D-n0dVsRuFoNW49906dsQOir8DnmYavSqIwvRnMNMvLc6dEBy1ks0nN8ybzO0f5MD/s1600/SJantzen-20190112_11617.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjh2J5mHDMB7503fo0Y5FhN57wsMmHYffYAAlBzJH3cm_2QGPzZk8ph07wmVvcVvpnP38l29-pP8I1D-n0dVsRuFoNW49906dsQOir8DnmYavSqIwvRnMNMvLc6dEBy1ks0nN8ybzO0f5MD/s640/SJantzen-20190112_11617.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">It's convenient that so much gaming hardware is perfectly functional for workstations.</td></tr>
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Then it was time to install the CPU. I chose the AMD Threadripper 2920x, with 12 cores, 24 threads, 3.5GHz base clock, and this post's namesake. For me it's a good balance of single- and multi-threaded performance and price. Screwing it down was a sweat-inducing nightmare though. I had to press hard way beyond comfort to get the tiny screws to catch. Installing the 64GB of Corsair RAM was comparatively easy, with 4 empty slots for adding more in the future. Yes, I use a lot of RAM hungry applications. There's simply never enough.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzj-xVUiLgpbI5Pxzvl84qjMEbVNahlx_wI4dCfV_HhuTBxUA9gfhVu1mA2HVAiiNWW7pdujIIAKoSauN7a8XH-uIhQfxqpztoRkYIQx_mQ0cbTaojD-fXHAwruOUIJbRzSiieAwZDsm3A/s1600/SJantzen-20190112_11627.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzj-xVUiLgpbI5Pxzvl84qjMEbVNahlx_wI4dCfV_HhuTBxUA9gfhVu1mA2HVAiiNWW7pdujIIAKoSauN7a8XH-uIhQfxqpztoRkYIQx_mQ0cbTaojD-fXHAwruOUIJbRzSiieAwZDsm3A/s640/SJantzen-20190112_11627.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This smallish piece of silicon came in the most dramatic packaging I've ever opened.</td></tr>
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Next is the "hard drive". In this case it's a tiny (half-terabyte) stick of non-volatile flash memory. Computer technology has come so far. The Samsung 970 series of NVMe SSDs is a very popular choice. I'm using this to hold my operating system (Windows 10 Pro) and all my applications (too many to list, sorry not sorry).<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWqXrhvVdijUqqgNrw067gjF28DQimSd5eGMF7MDfxK2EeVdECYkZax3dv_UPzRcL1jdJifWZ_V0pytlDO1UMA1zDc21Ru9OA_xBF1X0w8LpY1f-1shB5sqqDmKF0AoFkI7wcYB4R2xEfk/s1600/SJantzen-20190112_11631_long.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="608" data-original-width="1080" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWqXrhvVdijUqqgNrw067gjF28DQimSd5eGMF7MDfxK2EeVdECYkZax3dv_UPzRcL1jdJifWZ_V0pytlDO1UMA1zDc21Ru9OA_xBF1X0w8LpY1f-1shB5sqqDmKF0AoFkI7wcYB4R2xEfk/s640/SJantzen-20190112_11631_long.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">I broke one of the stand-off posts, I think. Ah well, not critical I'm sur&#,%20&..#^@.......</td></tr>
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I stuck with air-cooling for this build; I'm not quite convinced of the merits of water-cooling (even AIOs) just yet. Noctua has built great coolers for me in the past, and this giant hunk of metal looks to be another excellent cooler. I meticulously followed the thermal paste application guidelines; indeed I measured out and drew reference circles on that piece of paper in the image, to verify my pea-sized dots of paste.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiOZ87a7i0hU0WGt0zrrrcn-Vj_iRf7MGMNGXUAU3BT_1jCfRJ5373YVSiDcU4pPtnZ0J0HCvsCWZ7xHX3qlcVcbHZfv3hj3dNWJZwwcpSy_bX9wcuC4rsgfCx99mnrVsCFj6DcLiRnTg_/s1600/SJantzen-20190112_11640.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiOZ87a7i0hU0WGt0zrrrcn-Vj_iRf7MGMNGXUAU3BT_1jCfRJ5373YVSiDcU4pPtnZ0J0HCvsCWZ7xHX3qlcVcbHZfv3hj3dNWJZwwcpSy_bX9wcuC4rsgfCx99mnrVsCFj6DcLiRnTg_/s640/SJantzen-20190112_11640.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fans are available in beige and brown. No, beige AND brown.</td></tr>
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As mentioned previously, I'm using a GPU render engine called Redshift to create my images, so a decently powerful NVidia graphics card is a must. This one is the RTX 2070, and I also added the GTX 970 from my old computer (not pictured).<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQlbKctOJf9fvDhCBPcvcFglzsIYKtc9t8A3HtwMchUCxRku0wVJvRm0g4JQoU0LYRuxmmIn5xlOrYpaP9oCW5TLZuRZdPSMaZHTIpfgGRJZmUVpqQM4bofQRYoTPRSWDah20eVui5C0B_/s1600/SJantzen-20190115_11648.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQlbKctOJf9fvDhCBPcvcFglzsIYKtc9t8A3HtwMchUCxRku0wVJvRm0g4JQoU0LYRuxmmIn5xlOrYpaP9oCW5TLZuRZdPSMaZHTIpfgGRJZmUVpqQM4bofQRYoTPRSWDah20eVui5C0B_/s640/SJantzen-20190115_11648.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Blower-style. That's not a joke, that's what it is.</td></tr>
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I have to power all those components somehow! I wanted high efficiency and enough headroom to potentially add more graphics cards in the future, so the Corsair HX-1000 (1000W) seemed a good reliable choice.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEvAtiZlxeChAQBOH6tTwY9S98ToKftHqsDCbs8mqYHDAfyO9QtGeA0EjHhtUcLXymgrX8FqQjTSUCbY_0qRfN5CXPX7IkSQgMx4KSNuNFbQFM8oX3DmMRzttMHwNZ8NYJIjESKNPENJsC/s1600/SJantzen-20190112_11611.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEvAtiZlxeChAQBOH6tTwY9S98ToKftHqsDCbs8mqYHDAfyO9QtGeA0EjHhtUcLXymgrX8FqQjTSUCbY_0qRfN5CXPX7IkSQgMx4KSNuNFbQFM8oX3DmMRzttMHwNZ8NYJIjESKNPENJsC/s640/SJantzen-20190112_11611.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The computer component most likely to explode, kill you, catch on fire, or all of the above. Buy reliable.</td></tr>
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And… with held-breath, I poked the start button. And lights came on! And fans spun! And the BIOS showed up on my monitor! I checked a few things, flashed the BIOS to the most recent version so that my processor was properly supported, and shut it down again.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdBG4C5PiZQjRFrozAq_2pf_pnm1irDrKteT6LLvthfMCJ0ePPAAWvROXTUwJqdJd7Q8Je0wXhHNaf_VeVdFMIFlL3dCUTA-J0Dv4uMEdQjXCC80e82jjLjiSROXVTeyTW21r9NLixSNRM/s1600/SJantzen-20190112_11647.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdBG4C5PiZQjRFrozAq_2pf_pnm1irDrKteT6LLvthfMCJ0ePPAAWvROXTUwJqdJd7Q8Je0wXhHNaf_VeVdFMIFlL3dCUTA-J0Dv4uMEdQjXCC80e82jjLjiSROXVTeyTW21r9NLixSNRM/s640/SJantzen-20190112_11647.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The CPU fan started and stopped a bunch and freaked me out.</td></tr>
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Cut to a few days later when my case arrived. Actually it got dropped at a postal outlet many blocks away so I lugged it home in the snow because I'm cheap and don't like taxis and don't have Uber/Lyft and whatever. And exercise is good. The Fractal Design Define R6 Blackout without side-window with USB-C top panel (there are a lot of different configurations) was my choice of case and I'm pleased with it. It's a very understated and quiet black metal box. One would hardly know there's anything happening under my desk right now.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhREMRlybTyk8dPBhJRi2aXdpaQ-LEejotNoZtMhx9VRb5KfJ0_qd8IlBv1xGdTgOx521QCZJsWMLDsF2uc5yFfsl8SqEU5f06eV5O7QgmkXm0p5eEH3prNIBCp5Jo0E1GWHHccqOhJABrV/s1600/SJantzen-20190115_11653.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="607" data-original-width="1080" height="358" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhREMRlybTyk8dPBhJRi2aXdpaQ-LEejotNoZtMhx9VRb5KfJ0_qd8IlBv1xGdTgOx521QCZJsWMLDsF2uc5yFfsl8SqEU5f06eV5O7QgmkXm0p5eEH3prNIBCp5Jo0E1GWHHccqOhJABrV/s640/SJantzen-20190115_11653.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">It's bigger than it looks. But I didn't go crazy and get a Corsair 1000D.</td></tr>
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I finished the assembly inside the case and made sure the system still booted. It did, yay!<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8BhGRd7gL6RusUtkK7u6BKckvm2RZOapU5nlTJbBrtL4kPH7QTOkIrs04rxWcwNwxHvBFjkFE3zcrdqOPs05UniSlaZbJPEh-KNFMwtTQdkc5VEPu5mrLCX2ksKkw3R8uIG_-Ja5GcFl7/s1600/SJantzen-20190115_11657.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8BhGRd7gL6RusUtkK7u6BKckvm2RZOapU5nlTJbBrtL4kPH7QTOkIrs04rxWcwNwxHvBFjkFE3zcrdqOPs05UniSlaZbJPEh-KNFMwtTQdkc5VEPu5mrLCX2ksKkw3R8uIG_-Ja5GcFl7/s640/SJantzen-20190115_11657.jpg" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">If you see blue and red, your computer's not dead.</td></tr>
</tbody></table>
After installing and updating Windows, drivers, and some applications, I moved my hard drives from my old computer to the new system (2 SSDs and 2 HDDs) and did a bunch of cable management. I've been using this new machine for the past few weeks, getting everything installed and configured, and I must say I am very happy with the new system. I haven't pushed it too hard yet beyond some initial benchmarks and mini projects, so the biggest noticeable difference so far has simply been the noise. It is so much quieter than my old machine, it's hard to believe.<br />
<br />
And that's it! I'll need to upgrade my monitors and mouse (circa 2007-2008) next, but that can wait another few months or years.<br />
<br />
I hope with this post I struck the right balance of detailed enough but not boring. If you're down here instead of on <a href="https://www.instagram.com/biocinematics/" target="_blank">Instagram</a>, then perhaps it was okay. I'm happy to answer any and all questions via blog comments, <a href="https://twitter.com/biocinematics" target="_blank">Twitter</a>, <a href="https://www.instagram.com/biocinematics/" target="_blank">Instagram</a>, Email (stuart at biocinematics d0t com), or <a href="http://www.youtube.com/user/biocinematics" target="_blank">wherever</a>. You know: "Stuart, you simply must tell me, is your VRAM GDDR6 or HBM2???"<br />
<br />
Teaser: My next post will the last one on this blog. What? Why? How? Wherefore? Come back next week!<br />
<br />
Thank you for reading.<br />
Stuart<br />
<div>
<br /></div>
Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-39837557932307479042019-02-15T17:39:00.000-05:002019-02-15T17:49:48.290-05:00Knots and Robots<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I've made
various promises to share some recent work, and it's high time I follow-up on
that. Over the past few years, I've done a number of freelance animation and
illustration jobs, mainly for Professor David Leigh, who runs a <a href="http://catenane.net/">Chemistry laboratory at the University of Manchester</a>.
</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">On
several occasions I've been privileged to be able to work alongside this
research group, who perform intriguing research in the field of molecular
robots and molecular knots (What are those? See below for some more
explanation). My contributions have been primarily visual analogies of the science
behind their work.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I
designed editorial illustrations to generate interest in the research and for
use as cover images of the journals in which the research is published. I
shared one example in <a href="https://biocinematics.blogspot.com/2019/02/and-now-for-something-almost-completely.html">my previous post</a> and here's another example on the subject of molecular knots:</span><br />
<span style="font-family: inherit;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTXBkwlJjkmvZImK9jIunn9FkNM5FZgEbswSI3msZgwlJBb4xCNbKltva_iNVXhpk0sojyVbyCgMjQ3hqJeQ4ACbm-8MUgUaxlCMYAMA9H3LvP0yKAvgXbDEgFosLfVGA5iVlnmOYDy4GB/s1600/Knot_Cover_instagram.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto; text-align: center;"><span style="font-family: inherit;"><img border="0" data-original-height="1080" data-original-width="1080" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTXBkwlJjkmvZImK9jIunn9FkNM5FZgEbswSI3msZgwlJBb4xCNbKltva_iNVXhpk0sojyVbyCgMjQ3hqJeQ4ACbm-8MUgUaxlCMYAMA9H3LvP0yKAvgXbDEgFosLfVGA5iVlnmOYDy4GB/s640/Knot_Cover_instagram.jpg" width="640" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">An eight-crossing molecular knot and some ions</span></td></tr>
</tbody></table>
<div lang="en-US" style="margin: 0in;">
What's a
<a href="https://en.wikipedia.org/wiki/Molecular_knot">molecular knot</a>?
And why tie one? It's essentially a looped molecule that isn't just a loop. So…
it loops through itself <a href="https://en.wikipedia.org/wiki/Trefoil_knot">at least a few times</a>. There's an interesting (to me) <a href="https://www.youtube.com/watch?v=aqyyhhnGraw">mathematical field of knots</a>, where different kinds of knots are classified
based on numbers of crossings–and I probably shouldn't get too far down this
rabbit hole. So why create a molecular knot? In my mind, it's about finding
novel ways of chemically synthesizing new structures, which could be useful in
materials science, manufacturing, and nanotechnology.</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">It seemed
logical to depict this particular molecule as a knotted rope, and I went with a nautical
theme, including a central chloride ion represented as a Japanese glass fishing
float. To get the right feeling of a heavy, thick rope, I spent a long time
working with displacement maps to get the right texture, and I scattered loose
hairs with a MASH network.</span><br />
<span style="font-family: inherit;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp7XCdfbRsXHNQyKgNraZ38Mo-kAfoKhTA14oq2C9pfcoMny4EI_h2EW0khauvAszmMtoWJtVODWctJs_G9Hr3lcx7DYAXqxCsdeG1_QetJaaD8sDIqtjkbJdeA_DNFMRlTQUay2QX6A0I/s1600/rope_texture_hairs_01.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><span style="font-family: inherit;"><img border="0" data-original-height="862" data-original-width="675" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp7XCdfbRsXHNQyKgNraZ38Mo-kAfoKhTA14oq2C9pfcoMny4EI_h2EW0khauvAszmMtoWJtVODWctJs_G9Hr3lcx7DYAXqxCsdeG1_QetJaaD8sDIqtjkbJdeA_DNFMRlTQUay2QX6A0I/s640/rope_texture_hairs_01.png" width="501" /></span></a></div>
<div lang="en-US" style="margin: 0in;">
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">The
illustration didn't end up on the cover of Science, sadly (these choices are
made by the publisher for various reasons), but it did show up on various sites,
from <a href="https://www.forbes.com/sites/carmendrahl/2017/01/13/chemists-have-braided-molecules-to-make-the-tightest-knot-ever">Forbes</a> to <a href="https://www.npr.org/sections/thetwo-way/2017/01/12/509353074/scientists-have-twisted-molecules-into-the-tightest-knot-ever">NPR</a> and was an "Image of the Day" for <a href="https://www.the-scientist.com/image-of-the-day/image-of-the-day-tied-up-32206">The Scientist</a> and <i>apparently</i> <a href="https://twitter.com/Biocinematics/status/1050941864432594949">appears</a> in the 2019 Guinness Book of World Records, for the entry
"<a href="http://www.guinnessworldrecords.com/world-records/468343-tightest-knotted-structure">Tightest knotted structure</a>".</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Following the creation of an illustration, I was often tasked with developing short
animations to be used in presentations of the research. This knot synthesis
animation was a huge technical challenge, but a rewarding project. </span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-family: inherit;"><iframe width="640" height="360" src="https://www.youtube.com/embed/FpiC4ds_bkM" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">If I remember correctly, I ended up using three or four different rope rigging setups to create the necessary
behaviours as the lengths of rope assembled themselves.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiG9kmZA1_qc8J_ecbozJTUZ__uvNIMGjbpCOxtFtvogKJB41YNN_TcsCRWn72Yu_VDpnPDOmLpjbkZx-bp1mNcSRbgjdcBtji-e5egSjxvs3EscS5_VqJ756_4WYcbEUkQ29i6dp_0OZIZ/s1600/knot_mess.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: inherit;"><img border="0" data-original-height="723" data-original-width="889" height="520" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiG9kmZA1_qc8J_ecbozJTUZ__uvNIMGjbpCOxtFtvogKJB41YNN_TcsCRWn72Yu_VDpnPDOmLpjbkZx-bp1mNcSRbgjdcBtji-e5egSjxvs3EscS5_VqJ756_4WYcbEUkQ29i6dp_0OZIZ/s640/knot_mess.PNG" width="640" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">A technical mess looking like the proverbial Gordian Knot</span></td></tr>
</tbody></table>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">One of
the hardest parts, as you might imagine, was the binding action and getting the rope
"tendrils" to wrap around each other; I had to carefully measure
how far each rope-end was from its neighbours to get the action correct.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEico2EF9qOqlfGnelc28Mx0QE4KQwu87GzmG7iFIDu0wTlbY_PQKHsZJQ5VDZ11Jnx-fBC16l3W3eJUdu3Gaju2xwNKPwWjaoXqtBg_786Fq39dn-3I3k905xhu4apxs9on8vkqn5yr5dzj/s1600/Rope_rigs.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><span style="font-family: inherit;"><img border="0" data-original-height="799" data-original-width="873" height="584" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEico2EF9qOqlfGnelc28Mx0QE4KQwu87GzmG7iFIDu0wTlbY_PQKHsZJQ5VDZ11Jnx-fBC16l3W3eJUdu3Gaju2xwNKPwWjaoXqtBg_786Fq39dn-3I3k905xhu4apxs9on8vkqn5yr5dzj/s640/Rope_rigs.PNG" width="640" /></span></a></div>
<div lang="en-US" style="margin: 0in;">
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">In addition to the "knot" work, I also
ended up doing a few "molecular robot" pieces. One robot that the lab developed was capable of moving a cargo molecule from
one binding site to another, controlled purely by the addition of different
chemicals, such as certain acids and bases.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div style="text-align: center;">
<span style="font-family: inherit;"><iframe allowfullscreen="" frameborder="0" height="360" mozallowfullscreen="" src="https://player.vimeo.com/video/209313688" webkitallowfullscreen="" width="640"></iframe>
</span>
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">But what
does this robot actually look like? Well, we can't observe molecules of this size
directly, but here's the chemical structure, showing all the atoms that
comprise it.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZTbFrpCkKDTVzri1VgZJyAjyZ43OZALWEpjeEiLQTUl7pnCndUaFmNs6YcnLDKygLGDSWWXVohLeOYh-Xy1Jqoz2D8SOg2RvjuQjGZZ_BwsyEsFR60LUXdWaHe8dXQ02WI7Re1Vs8OKsi/s1600/Robot_chemical_structure.png" imageanchor="1" style="margin-left: auto; margin-right: auto; text-align: center;"><span style="font-family: inherit;"><img border="0" data-original-height="498" data-original-width="774" height="256" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZTbFrpCkKDTVzri1VgZJyAjyZ43OZALWEpjeEiLQTUl7pnCndUaFmNs6YcnLDKygLGDSWWXVohLeOYh-Xy1Jqoz2D8SOg2RvjuQjGZZ_BwsyEsFR60LUXdWaHe8dXQ02WI7Re1Vs8OKsi/s400/Robot_chemical_structure.png" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">You can see why I used a lot of hexagon motifs</span></td></tr>
</tbody></table>
<div lang="en-US" style="margin: 0in;">
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">The lab
developed this concept further and designed a programmable molecular robot with
a similar structure to the one above. This new molecule can synthesize different stereoisomers, driven once
again by different chemical reagents. What are stereoisomers? They are
sets of related molecules that differ only in the 3D orientation of atoms. So
think of one molecule having an atom sticking out the front,
and its "stereoisomer" partner has the corresponding atom sticking
out the back.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<iframe width="640" height="360" src="//www.youtube.com/embed/GInuclG3KTM" frameborder="0" allowfullscreen></iframe>
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I had an
early concept for a delivery system for the atoms (shown as colored balls in the video), which I
think is kind of fun, but we ended up with a simpler concept where the atoms just fly to the tables.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguR93zTJUKaA-0SsFGU0zXeZdGHE51lTPIXJeblsOKjExfQpM6iU1HnSbRKV8MMmmiingvSECxZ1ztreTi_mzggLjHU02TPslZfqU2Zkr58TQu1kCQ3LbPFf3qO1vJl6kkGo3jbEUGu7L-/s1600/table_blocking_animated.gif" imageanchor="1" style="margin-left: auto; margin-right: auto; text-align: center;"><span style="font-family: inherit;"><img border="0" data-original-height="566" data-original-width="775" height="291" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguR93zTJUKaA-0SsFGU0zXeZdGHE51lTPIXJeblsOKjExfQpM6iU1HnSbRKV8MMmmiingvSECxZ1ztreTi_mzggLjHU02TPslZfqU2Zkr58TQu1kCQ3LbPFf3qO1vJl6kkGo3jbEUGu7L-/s400/table_blocking_animated.gif" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;"><br /></span></td></tr>
</tbody></table>
<div lang="en-US" style="margin: 0in;">
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I also
had fun designing the peripheral apparatuses (apparati?) to fit with the mechanical theme:</span></div>
<div lang="en-US" style="margin: 0in;">
</div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJ0ZYnVemXkAFh1HIYfO6MKYA42OwVec_QdPJRA36tXA3-TbLSvvVkoiBpJSrbLAx3ucVFEqoZPEvOvQSzna9-L54rRi6GCI9L_BTwz342ki5uuCmFgUmjk2OSgjZtN2ZJXbfXbSoYnIV0/s1600/entry_hatch_retracted_and_extended.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: inherit;"><img border="0" data-original-height="810" data-original-width="1053" height="492" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJ0ZYnVemXkAFh1HIYfO6MKYA42OwVec_QdPJRA36tXA3-TbLSvvVkoiBpJSrbLAx3ucVFEqoZPEvOvQSzna9-L54rRi6GCI9L_BTwz342ki5uuCmFgUmjk2OSgjZtN2ZJXbfXbSoYnIV0/s640/entry_hatch_retracted_and_extended.png" width="640" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">Substrate entry...</span></td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_NSTFHX_6QvlOiVbYsahUu5X5YA_kAyKZu8efndcYDT4obONhG22V2J4QOOb2HPSU-yp97cZoYW1cPL_K15BNVI7OL8R3kILXXJD5B6DZlcagAY_XXfyFtkBXXeSiXzAjdRHccamVXUUa/s1600/exit_hatch_open.png" imageanchor="1" style="margin-left: auto; margin-right: auto; text-align: center;"><span style="font-family: inherit;"><img border="0" data-original-height="810" data-original-width="1440" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_NSTFHX_6QvlOiVbYsahUu5X5YA_kAyKZu8efndcYDT4obONhG22V2J4QOOb2HPSU-yp97cZoYW1cPL_K15BNVI7OL8R3kILXXJD5B6DZlcagAY_XXfyFtkBXXeSiXzAjdRHccamVXUUa/s640/exit_hatch_open.png" width="640" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">... and chemical product exit</span></td></tr>
</tbody></table>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will conclude this lengthy post here (granted much has happened in the last couple
years). Thanks for reading all the way down here. Next week I'll share some
details about my new workstation, which may be of interest to some?</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Finally, an optional "Call to
Action": If you'd like to help me out tremendously, subscribing to my
<a href="https://www.youtube.com/user/biocinematics">Biocinematics</a> channel and liking the most recent two videos (if indeed that aligns with your feelings
towards them) would be massively appreciated. If you have already have a Google account or
Gmail account, you don't need to sign up for anything new or take any extra
steps. If you'd like to go the extra mile, you could share this YouTube channel
with friends or family who might be interested in educational science-y stuff.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Thanks
again for reading and supporting me,</span></div>
<div lang="en-US" style="margin: 0in;">
<br /></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Stuart</span></div>
Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-52493364522942184022019-02-08T16:20:00.000-05:002019-02-08T16:32:45.151-05:00And now for something (almost) completely different<span style="font-family: inherit;">Hello
again! It's been a little while. Okay, two and a half years.</span><br />
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Way back
in 2016, I started working at <a href="https://axs3d.com/">AXS Studio</a> (see <a href="https://biocinematics.blogspot.com/2016/08/molecular-monday-mornings-in-maya-and.html">announcement from my previous post</a>).
As a technical artist / technical director, I worked on: illustrations,
including one for <a href="https://www.scientificamerican.com/article/ingestible-robots-perform-surgery-from-inside-the-body/">Scientific American</a>;
animations, including clips for a <a href="https://www.youtube.com/watch?v=5E266unLT3Q">PBS documentary</a>; and interactive projects, including a <a href="https://guardiansofthegenome.com/">multiplayer VR game</a>
about repairing DNA as nanobots.
I also worked on a lot of technical aspects: designing effects and rigs,
managing a render farm, programming animation tools, fixing broken assets, and
many more.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div style="margin: 0in;">
<span style="font-family: inherit;"><span lang="en-US">Over
the past couple of years, I also worked freelance on a number of animations and
images for Professor David Leigh (</span><a href="http://catenane.net/"><span lang="en-US">http://catenane.net/</span></a><span lang="en-US">), which I will share
more about in a follow-up post next week. </span><span lang="en-US">In the meantime, you
can see some of the work on my website (</span><span lang="en-US"><a href="https://www.biocinematics.com/">www.biocinematics.com</a>)</span>. <span lang="en-US">This
is an illustration that was created for Nature (submitted for the cover, but sadly not used as such) in
which a </span><span lang="en-CA">programmable molecular machine is depicted as a
robotic arm. The molecule can produce different stereoisomers depending on the sequence of chemical inputs.</span></span></div>
<div style="margin: 0in;">
<span lang="en-CA" style="font-family: inherit;"><br /></span></div>
<div style="margin: 0in;">
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6ZIVLgYlPhXhLP4v0D9PaDnhUPWtB88ceuSUgkg09KaXR5V6W-LJAk0xtD6i0SiMZ155QWjKzNeYGkvf7zrSV_PWAOTFLj6O_wkOrQFyPHpIT_LYsWqk3CJt58JCOXCYddtCUbK0qw_kc/s1600/Jantzen_BCM_Stereoisomer_Cover_web_1280.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: inherit;"><img border="0" data-original-height="1279" data-original-width="919" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6ZIVLgYlPhXhLP4v0D9PaDnhUPWtB88ceuSUgkg09KaXR5V6W-LJAk0xtD6i0SiMZ155QWjKzNeYGkvf7zrSV_PWAOTFLj6O_wkOrQFyPHpIT_LYsWqk3CJt58JCOXCYddtCUbK0qw_kc/s640/Jantzen_BCM_Stereoisomer_Cover_web_1280.jpg" width="458" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">Programmable molecular robot</span></td></tr>
</tbody></table>
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">Over the
last few months, I came to the difficult decision to leave AXS Studio and
pursue some self-directed work. Why? There are a number of reasons: some
personal and family-related, others professional. Ultimately, I decided the
time was right to try something (almost) completely different.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Since
before this blog started (nearly 10 years ago!) I've been passionate about
using animation and computer visualization to teach people about molecular
biology. That has not changed, and now more than ever, that's exactly what I
want to do. However, the format, platform, technology, and job description will
be new to me. More on that in a moment.<span style="mso-spacerun: yes;"> </span>I realized that to educate and inspire people (especially young people)
and help them engage in biology, I need to forego the client-work and studio-work models typically used in the field of biomedical illustration/animation.
There's a lot I'd like to explore within science education, so at least for the
next year, I'm giving myself free reign to create whatever I feel will best express
the ideas I have about biology, education, and animation.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Well,
that sounds very lofty and vague, but what am I actually going to do? Some of
it is TBD, that's kind of what "free reign" means. But here's the
elevator pitch:</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will be
making videos about biology.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">They will
be a combination of 2D and 3D animation, with maybe some video footage. Let's
call it "mixed media".</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">They
won't all be the same format, length, style, structure, or content.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">They will
be on YouTube, all freely accessible for everyone that has open internet
access.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">They will
be less about facts and more about concepts. I want to promote understanding
more than knowledge of trivia.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">They will
be fun and maybe sometimes a little funny.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Also:</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will continue to publish tutorials, though I expect to migrate them to a
second channel in the near future.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will be
creating editorial molecular illustrations on <a href="https://www.instagram.com/biocinematics/" target="">Instagram</a> and <a href="https://www.biocinematics.com/" target="">my website</a>.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will
continue to post on this blog.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will be
learning a lot of new things (see below).</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will likely work on the occasional freelance client project.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I will
likely have some other interesting side projects on the go. We'll see what
comes up.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">I know,
that looks like a lot. It is a lot. It's ambitious and risky, and I could fall
down and embarrass myself and have to find another "real job" and
that's okay. It's really okay. This is a journey I need to take regardless of
where it leads, and I'm incredibly excited to start down these paths.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Is there
anything else new?</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Yes, I
built myself a new computer. I'll write a blog post about it down the road.
It's awesome and fun and I haven't had a new workstation at home since
TWO-THOUSAND-AND-NINE. Yes, that's right, since the year this blog started.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">I'm going to be doing a lot of reading and research in molecular biology - to refresh my undergraduate knowledge, to fill in some gaps, and to deepen my understanding of physical biology, biochemistry, and related disciplines. My bookshelf is now overstuffed with textbooks.</span><br />
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">And I'm
going to be using a lot of new software. Some of it I've used a little, some a
moderate amount, and some none at all. Here's my
current pipeline plan:</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Reference
management: Zotero</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Writing:
Sublime</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Storyboarding:
Storyboarder</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Modeling:
ZBrush/Houdini/Blender</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Animation/FX:
Houdini</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Texturing:
Photoshop/ZBrush</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Rendering:
Redshift</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Compositing:
Fusion</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Motion
Graphics/Titles: AfterEffects/Illustrator</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Editing/Grading:
DaVinci Resolve</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">SFX/Music:
Ableton Live/DaVinci Resolve</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Where's
Maya in this mix? For various reasons, I am gracefully disembarking from the
Autodesk and Adobe trains. By gracefully, I mean I'm taking a giant leap and
trying to remember how to do a tuck-roll. It's true, I will be making some use
of my Adobe CS6 collection, but I think the time has come to step away from
Maya. It's been fun, and I may come crawling back, but this is another area in
which I need to assert some independence and do what I believe is right for me.
Wow, that got a little personal. Moving on…</span><br />
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihZeGjRPj8lki9B6cVi2r36V5qQUEyjp0RnRkylD1I33d2EF3_xj1FuEu3iW9_t3seRJ_3myt8ffjhRiD2eKKNj6J30Kg4PTSIZDPV40Th2ZbHYg6Z8cnjIy-E8xFQHapcgVY8m7FEoHPL/s1600/Jantzen_Houdini_Redshift_train_test.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: inherit;"><img border="0" data-original-height="720" data-original-width="1280" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihZeGjRPj8lki9B6cVi2r36V5qQUEyjp0RnRkylD1I33d2EF3_xj1FuEu3iW9_t3seRJ_3myt8ffjhRiD2eKKNj6J30Kg4PTSIZDPV40Th2ZbHYg6Z8cnjIy-E8xFQHapcgVY8m7FEoHPL/s640/Jantzen_Houdini_Redshift_train_test.jpg" width="640" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit; font-size: small;">Initial Redshift test in Houdini</span></td></tr>
</tbody></table>
<span style="font-family: inherit;">Houdini
and Fusion/DaVinci Resolve are the big new ones for me. They both have steep
learning curves, but there are several reasons I think they are good choices
for content creation for me. It's a bit premature to get into all of that now,
but I'm sure I'll end up talking about it in the future.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">This has
been, by necessity, a fairly long post, so I'll try to wrap it up here.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">Thanks
for reading, and I hope you'll stay in touch as my new adventures begin.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Stuart</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;">Ah… maybe
a very brief and slightly awkward <b>FAQ</b>:</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>Q:</b> Sorry
if I missed it, but are you planning to earn money? YouTube is a hard ecosystem
to succeed in.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>A:</b> Yes, I
know. I will be experimenting with various revenue streams, but regardless of
financial success, I'm in this for at least a year. I'll be doing the
occasional client gig on the side, but my focus is to create the animations
that I feel most passionate about.</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>Q:</b> I want
to support your efforts, what's the best way for me to do that?</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>A:</b> Aw,
thanks! For now, I'd love for you to subscribe to my <a href="https://www.youtube.com/biocinematics" target="">Biocinematics YouTube channel</a> and connect with me on the social media platforms you regularly use (Twitter: <a href="https://twitter.com/biocinematics">@biocinematics</a>,
Instagram: <a href="https://www.instagram.com/biocinematics/">@biocinematics</a>, Facebook: <a href="https://www.facebook.com/biocinematics/">@biocinematics</a> - consistency is good).</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>Q:</b> I
mean, is there any way to support you financially?</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>A:</b> What,
really? That's super kind. I couldn't possibly… *shuffles feet*. No, nothing
yet, but stay tuned. Keep an eye on the social media platform of your choice,
and I will be sure to make some noise once there are more things in place. Give
it a little time though, there's a chance you won't want to "buy what I'm
selling" after all…</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><br /></span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>Q:</b> Is the
post title a Monty Python reference?</span></div>
<div lang="en-US" style="margin: 0in;">
<span style="font-family: inherit;"><b>A:</b> …………….
Ni!</span></div>
Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-85028857304458928872016-08-23T20:28:00.002-04:002016-08-23T20:28:41.422-04:00Molecular Monday Mornings in Maya - and an AnnouncementI've started a new series of Maya tutorials on <a href="https://www.youtube.com/c/biocinematics" target="_blank">YouTube</a>. I'm not sure how long it'll last, but the first two installments are about using <a href="https://clarafi.com/tools/mmaya/" target="_blank">Molecular Maya</a> to work with <a href="http://www.rcsb.org/pdb/home/home.do" target="_blank">macromolecular structures</a>.<br />
<br />
The first deals with the challenge of importing very large molecular weight structures.<br />
<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/Rrov263BUps?rel=0" width="640"></iframe><br />
<br />
The second is more visually interesting, because we get to render some beautiful atoms.<br />
<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/CKAliNr-wKE?rel=0" width="640"></iframe><br />
<br />
The main problem I anticipate will prevent me from continuing this series is the fact that I have a NEW JOB! That's right, I will soon be leaving the academic world for the first time since I was a wee tot, and entering the... industry sector? That doesn't quite sound like the right term, but in any case, I will be joining the fine <a href="http://www.axs3d.com/" target="_blank">AXS studio</a>. I may have <a href="https://biocinematics.blogspot.ca/2011/02/im-going-to-toronto.html" target="_blank">mentioned them quite a while ago</a> on this same blog. I will be employed as a 3D Biomedical Technical Artist, which means I'll get to work in Maya on the things I most enjoy creating.<br />
<br />
So how might this prevent future tutorials? Well, so far I've used an educational license for tutorials that I've had access to through my institutional affiliation. But after I leave, I expect I will occasionally get a monthly license for freelance jobs, but mostly I may not have Maya at home. Which is very sad. Maybe an anonymous benefactor could finance a continued subscription for my home use. Anyone?<br />
<br />
This also reminds me that I should post some of the freelance work that I've done over the past year. How remiss of me.<br />
<br />
Thanks for reading (and watching),<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-18738289060614847762016-08-15T15:04:00.002-04:002016-08-15T15:06:00.598-04:00Website refreshThe new incarnation of my Biocinematics portfolio site and resource hub is now live (and has been for a few weeks), but in the business of conferences, holidays, and just getting the site pseudo-ready, my blog has been neglected. No longer! Perhaps. You may notice that the blog look has also been refreshed, and I aim to post more regular updates here again as I wrap up some old projects and start new ones.<br />
<br />
Get to the site by clicking in any number of places, see if you can find some of them. One is here: <a href="http://www.biocinematics.com/">http://www.biocinematics.com/</a><br />
<br />
And speaking of conferences, here is my conference presentation on Molecular Visualization.<br />
<br />
<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/G5FxPdBMUHE?rel=0" width="640"></iframe>Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-17492083487771066792016-03-17T17:02:00.002-04:002016-03-17T17:02:53.627-04:00Redshift<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHCeMrEGHZKFxdq-VgmrqX2FJaI_qkIzr0MVtg4iObiL-JbxQrnhTHBLtD7Muaj5JgbTOn2lbO2odIsOCCzByESdLH6uhNWV40OZyPh53r7nON5xOmMTqWstpjUPCDutRpryr3j4i04oS-/s1600/RasRaf_Redshift_Render.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHCeMrEGHZKFxdq-VgmrqX2FJaI_qkIzr0MVtg4iObiL-JbxQrnhTHBLtD7Muaj5JgbTOn2lbO2odIsOCCzByESdLH6uhNWV40OZyPh53r7nON5xOmMTqWstpjUPCDutRpryr3j4i04oS-/s640/RasRaf_Redshift_Render.jpg" width="640" /></a></div>
<br />
Well... it's been a while. Probably the longest gap in posting in the history of this blog, if you don't count the somewhat inane (albeit fun!) previous post.<br />
<br />
Why? Well the primary reason is because I've been planning a new website. My old site (http://bmc.erin.utoronto.ca/~stuart/) is "long in the tooth", was designed as a student site, and the school server it is hosted on is likely going to be shut down in the coming months.<br />
<br />
So, I've been trying to get a new site up and running (with a quantum of success so far) on Squarespace. You can check out the "coming soon" splash page: https://biocinematics.squarespace.com/<br />
Or maybe the site will already be live when you click through the link, in which case, yay!<br />
<br />
Squarespace has a reasonably robust blog system, so I was thinking that I would migrate this blogger blog to the new framework and continue posting from there. I tried a test import and everything went very smoothly. It went so smoothly in fact, that I didn't want to mess things up by creating new posts on the "old" platform which would need to be migrated on top of the original import. So I stopped posting here. But I also haven't progressed to far with getting the new site fully functional. Hence the silence.<br />
<br />
**crickets**<br />
<br />
Now, however, I've come to the realization that I really do like this blogger platform. It is familiar and functional and I've got so many stats, links, search rankings, etc. tied to this platform, that I would likely be taking a step backwards in visibility if I made the switch.<br />
<br />
So, I plan to stick with this platform, keeping the updates coming, while I continue getting the new site up. I want to do a bit of a cosmetic facelift on this blog once the styling for the new site has been established, to keep things looking cohesive.<br />
<br />
So, what about that render up there? I've been totally sold on a relatively new render engine called <a href="https://www.redshift3d.com/" target="_blank">Redshift</a>. It's fast and fun and suits my needs quite well. Check back in a bit for some new work using this renderer.<br />
<br />
Thanks for reading and for enduring the silence! Or at least, for not forgetting about me.<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com2tag:blogger.com,1999:blog-197012358288299042.post-8607319294833348742016-01-15T14:36:00.004-05:002016-01-15T14:58:11.575-05:00How to Play Wiki-Jumping<a href="https://15.wikipedia.org/index.html" target="_blank">Happy Birthday Wikipedia!</a><br />
<br />
I came up with a fun little game about five years ago that involves two people, at least three minutes of spare time, and <a href="https://en.wikipedia.org/wiki/Main_Page" target="_blank">Wikipedia</a>. I do recognize that others have independently arrived at the same or similar concepts, very likely before I did, so I'm not claiming any true originality, though I'm fairly sure I didn't hear about Wiki-Jumping prior to my idea. In fact I've come to see that <a href="https://en.wikipedia.org/wiki/Wikipedia:Wikirace" target="_blank">Wikiracing </a>is fairly established, and while that destroys any claim to fame I may have on the matter, it also validates my opinion that it is pretty good fun. Here is my version of the game and rules.<br />
<br />
The game is simple. Decide who will pick the start subject and who will pick the target/destination subject. Then each player thinks of a subject (thing, concept, person, animal, event, place) that is likely to be a wikipedia page. They simultaneously announce their subjects and both players navigate to the start subject page. On the command of "GO", the two players start clicking on in-page links, with the goal of arriving at the target page. The first person to arrive at the destination subject wins. Then spend an enjoyable minute clicking the back button to show each other your traversals.<br />
<br />
Formal rules:<br />
1) Both subjects should have a single unambiguous wikipedia page. This isn't too hard, but if you choose something like "<a href="https://en.wikipedia.org/wiki/Chicago_(disambiguation)" target="_blank">Chicago</a>", decide on the specific context (e.g. city, band, movie etc.).<br />
2) When playing, you may only click on links within the body of the wikipedia article that link to another wikipedia article. No external links, no sidebar clicks. You MAY use the contents feature, and the See Also section. You may not use <a href="https://en.wikipedia.org/wiki/Portal:Mathematics" target="_blank">Portals</a>.<br />
3) You may not use any search functions. Essentially, you may not use the keyboard.<br />
4) You may not use the back button. If you make an erroneous click, you'll have to find your way back by moving forward.<br />
5) If both players agree find they are stuck in a loop or can't make progress, you may agree to a draw.<br />
6) You may not look at each other's screens during the race, though you may volunteer information (e.g. "I'm at <a href="https://en.wikipedia.org/wiki/Non-Newtonian_fluid" target="_blank">Non-Newtonian fluid</a>!").<br />
<br />
I realize that this game may sound boring, nerdy, tedious, or just plain silly, but I guarantee that if you're the least bit competitive and creative, the game can be hilarious, nail-biting, and even fun for spectators. It involves strategy, wits, and of course it's free.<br />
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Happy Wiki-Jumping!<br />
<br />
PS Having trouble finding some subjects? Try these out:<br />
<a href="https://en.wikipedia.org/wiki/Golden_Gate_Bridge" target="_blank">Golden Gate Bridge</a> to <a href="https://en.wikipedia.org/wiki/Pi" target="_blank">Pi</a><br />
<a href="https://en.wikipedia.org/wiki/Sputnik_1" target="_blank">Sputnik 1</a> to <a href="https://en.wikipedia.org/wiki/Sushi" target="_blank">Sushi</a><br />
<a href="https://en.wikipedia.org/wiki/Golden_poison_frog" target="_blank">Golden poison frog</a> to the <a href="https://en.wikipedia.org/wiki/United_States_Declaration_of_Independence" target="_blank">American Declaration of Independence</a><br />
<a href="https://en.wikipedia.org/wiki/Abbey_Road" target="_blank">Abbey Road (album)</a> to <a href="https://en.wikipedia.org/wiki/Sea_level" target="_blank">Sea level</a> (Bonus challenge: Traverse this in 4 clicks or fewer)<br />
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PPS I've been a bit silent on this blog recently, not because I haven't been doing anything, but because I'm in the process of building a new website which will house my blog, and I'm working through migrating this blog over.Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-28005000465145074862015-10-08T16:35:00.000-04:002015-10-08T16:36:41.254-04:00Intro to Maya - More ScreencastsFour weeks into the course and there are literally hours of Maya training on YouTube now.<br />
Here's a few of the tutorials:<br />
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/gGsUpQzwUd8" width="640"></iframe><br />
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/AU3Z4KgnApg" width="640"></iframe><br />
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/ByXuOaI0m4A" width="640"></iframe><br />
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Thanks for visiting,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-15777903588734779852015-09-17T14:29:00.001-04:002015-09-17T14:29:16.917-04:00Intro to Maya - Course ScreencastsThis week I started teaching a Maya course, like the one I taught this past winter, except this is part one of the two. So here we're starting at the very beginning, opening Maya for the first time together.<br />
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/eN5BoQ2cr1Q?rel=0" width="640"></iframe><br />
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/j_WLnJNo9TU?rel=0" width="640"></iframe><br />
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After this class, the sessions will be much more biomedically focused. I generally start with some concepts, what I call "fiddling with primitives" and then move onto a step-by-step tutorial to create something. I won't post the videos here every week, so <a href="https://www.youtube.com/subscription_center?add_user=biocinematics" target="_blank">subscribe to my YouTube channel</a> to see the latest as the come up each week.<br />
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Thanks for visiting,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-32008966760853760792015-09-01T09:00:00.000-04:002015-09-01T09:00:02.401-04:00Cu-Al-FeCrNi_AuThe second in the series: Cu-Al-FeCrNi_Au<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2R3oirVYswXeXbXVkyOeHzs06JsPAgMsBy1lqrnLXrGkha8k3sT2ka7NeZIoBDH0salg-9qfMHH6JAsaTL0V9aVkuf7dFwD6W6wUBdfeDk1BkfggiAo1wwAIdropmIcEoScwL5L85iJek/s1600/Cu-Al-FeCrNi_Au.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="460" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2R3oirVYswXeXbXVkyOeHzs06JsPAgMsBy1lqrnLXrGkha8k3sT2ka7NeZIoBDH0salg-9qfMHH6JAsaTL0V9aVkuf7dFwD6W6wUBdfeDk1BkfggiAo1wwAIdropmIcEoScwL5L85iJek/s640/Cu-Al-FeCrNi_Au.jpg" width="640" /></a></div>
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Medium: ForeverSpin 2.0 tops with J. Herbin Emerald of Chivor 1670 Anniversary Ink on Acid-Free Sketch PaperStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-16686772037072318652015-08-31T09:24:00.000-04:002015-08-31T09:24:21.361-04:00Element 29Here's just a bit of fun. Some might call it fine art. I call it Element 29.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW_ELwMWV2O9es6YxWXs5Snj-Qyhqxwz7M0YJ5JV81hfjBeCEbklsTnhJ0qGHGB2rXSetH3Z5qYNSVpvD52va0GQD5oRwYt1mkBBmd2GmaknmsX_FOv0xgBIRp_8iqXfZtfYyzyVli9rCS/s1600/Element_29_BCM.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="494" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW_ELwMWV2O9es6YxWXs5Snj-Qyhqxwz7M0YJ5JV81hfjBeCEbklsTnhJ0qGHGB2rXSetH3Z5qYNSVpvD52va0GQD5oRwYt1mkBBmd2GmaknmsX_FOv0xgBIRp_8iqXfZtfYyzyVli9rCS/s640/Element_29_BCM.jpg" width="640" /></a></div>
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Medium: Copper ForeverSpin 2.0 with Noodler's Ink Black on Acid-free Sketch PaperStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-23503250836323694392015-08-22T11:17:00.002-04:002015-08-22T11:17:47.378-04:00Wireframe Contour Rendering with Maya 2016 and mental rayRendering a contour image in mental ray for Maya has been a nice way to show wireframes on an object. In Maya 2016 the usual method has become somewhat hidden, so I thought I would post a brief update on how to do that.<br />
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1) Create a black surface shader and apply it to your geometry<br />
2) In the hypershade, access the shading group (e.g. surfaceShader1SG) and open the mental ray tab in the Attribute Editor (or Hypershade property editor!)<br />
3) Under Contours, check Enable Contour Rendering and adjust the other options as you like<br />
4) In the render settings, make sure mental ray is selected, and go to the Configuration tab<br />
5) Check "Show Advanced Settings" and find the Contours section at the bottom<br />
6) Check "Enable Contour Rendering" and increase the Over-Sample to something like 3<br />
7) Under the "Draw By Property Difference" section, check "Around all poly faces"<br />
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Not quite done... you might see a Warning: Contour Rendering is not supported with Unified sampling<br />
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8) Go to the Quality tab and check "Show Advanced Settings"<br />
9) Expand the Legacy Options section at the bottom and choose Sampling Mode: Legacy Sampling Mode<br />
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Hit render! *phew*<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-OleFV87s9QOSLTyp2UHLQD7JyIWGfyWvrN5-JV1dt5wXA14rbx-hw2o-jh979w-N5PnwXTcTUv2WS-b1cqqhq0eUpRikualtQsRgYB-qU1zrFr2HzGgzL8C68Prurlc2DuEXLvRUKwl4/s1600/polygon_contours_01.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-OleFV87s9QOSLTyp2UHLQD7JyIWGfyWvrN5-JV1dt5wXA14rbx-hw2o-jh979w-N5PnwXTcTUv2WS-b1cqqhq0eUpRikualtQsRgYB-qU1zrFr2HzGgzL8C68Prurlc2DuEXLvRUKwl4/s400/polygon_contours_01.png" width="310" /></a></div>
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Note that if you are rendering beauty passes or other things, you probably want to use the original Unified Sampling and just create layer overrides for the contour settings. Also make sure that you have unchecked both "Around all poly faces" and "Enable Contour Rendering" for these non-contour passes/layers/renders, because I have had the filter settings be set to Box (1, 1) in the background without my knowledge due to "incompatibility with contour rendering". Just something to be cautious about; not sure if they may have fixed that in this version.<br />
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Thanks for reading,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com15tag:blogger.com,1999:blog-197012358288299042.post-5481680851832302782015-07-29T14:30:00.000-04:002015-07-29T14:30:02.706-04:00Strange TeapotI've been learning how to use <a href="http://renderman.pixar.com/view/renderman" target="_blank">Pixar's Renderman</a> for shading, lighting, and rendering. I was trying to get a handle on setting up different shading networks, so I decided to go a bit crazy while I figured out how to use various nodes. This was the rather unfortunate result.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_XI94CgLXbcRN5ZNIFXmIkxi0CvAuRZhltkWa184vHXkf51NTAOd58Ornn3TOOn5kjDTDL5hBc7g0DEiJTJA0RVg9cDhPvhjt_30v5abmKpOrExI_JmGp-Tf6rwqXQru66PoAlkUUB22k/s1600/shading_network_testing.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_XI94CgLXbcRN5ZNIFXmIkxi0CvAuRZhltkWa184vHXkf51NTAOd58Ornn3TOOn5kjDTDL5hBc7g0DEiJTJA0RVg9cDhPvhjt_30v5abmKpOrExI_JmGp-Tf6rwqXQru66PoAlkUUB22k/s640/shading_network_testing.jpg" width="640" /></a></div>
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I used the <a href="https://community.renderman.pixar.com/article/231/the-official-renderman-swatch.html" target="_blank">Official RenderMan Swatch</a> (aka the renderman teapot) to play around with. I learned how to work with displacement, bump, blend, and facing ratio nodes, various noise textures, and the layered shader.<br />
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Thanks for visiting!<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-47784963756992517362015-07-27T21:02:00.000-04:002015-07-27T21:02:35.471-04:00Science Photography EdX Course - Week 5<div class="separator" style="clear: both; text-align: left;">
Though this is the penultimate week in the online course I've been taking, I believe this is the final assignment. Choosing one (or more) of the images we captured during the course, we were to create an educational figure from it. This was up my alley, so to speak, and I broke out the leader-lines and orientation images. I'm fairly happy with how this turned out. I think the leader-lines are a bit thicker than necessary, and though I like that everything is neatly aligned, I don't think the text sticking out to the left works as well. </div>
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It's also not a complete educational figure, since it only shows some of the mechanisms in the watch, but these were the images I had available, and I'm not quite ready to completely deconstruct the pocket watch.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2S6wabVwYtoBXev3C38cxWtgWsHDmqv17ODAy6AkXjtimZj3tTUFK5DsrwQNRz8jTTtkwDS7aE6i-dJH1OnbhYB8zxadwpSGYIGRiNehoIVI-_q6Z66c5kjAPzkacNudvzrq3FTfPtVA9/s1600/Jantzen_S_Figure_Expert_01.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="588" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2S6wabVwYtoBXev3C38cxWtgWsHDmqv17ODAy6AkXjtimZj3tTUFK5DsrwQNRz8jTTtkwDS7aE6i-dJH1OnbhYB8zxadwpSGYIGRiNehoIVI-_q6Z66c5kjAPzkacNudvzrq3FTfPtVA9/s640/Jantzen_S_Figure_Expert_01.png" width="640" /></a></div>
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I've really had an excellent time with this course and been exposed to many ideas that will serve me well not only in my photography, but also in the computer graphics I'll be doing in the future. And I've been inspired to do more macro photography, so if you're at all interested in that, perhaps keep an eye on this space and we'll see what turns up.<br />
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Thanks for reading!<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-60706826935783467012015-07-20T18:47:00.000-04:002015-07-20T18:47:00.043-04:00Science Photography EdX Course - Week 4This week's assignment had two components relating to mobile phone cameras and video.<br />
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The first part asked the students to spend a day taking photos around the house or at work with one's smartphone. I'm not too enthused with my phone's camera, but it was an interesting assignment to think about where photographic subjects might be. It was easy to grab a quick snap of an interesting texture, the way light fell on a mundane object, or how this item looked at a different angle. I'll consider using my phone as a brainstorming tool, then perhaps go in with my better camera and explore the subject further.<br />
Here are the two images I thought were most interesting:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDkpyDUkZE8gG4ehWFnEi5cFIarWVYGx7JFshhqCbCVDnEw2m9drDqHlLdyCJZXpm_rh1m03RZR5htv2b_-ppkCWvHKZ7NXAOr8lOuzPXvBMNKmXF8a1Y0F45JnKxkkv5imVKlbl0zK8B_/s1600/SJantzen-bracket_Week4_02_full.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="348" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDkpyDUkZE8gG4ehWFnEi5cFIarWVYGx7JFshhqCbCVDnEw2m9drDqHlLdyCJZXpm_rh1m03RZR5htv2b_-ppkCWvHKZ7NXAOr8lOuzPXvBMNKmXF8a1Y0F45JnKxkkv5imVKlbl0zK8B_/s640/SJantzen-bracket_Week4_02_full.jpg" width="640" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhPrNjy39CxU8i-OJTsEo0fzTBCZEkGrdcLX_wKbDP7B0lzCkiBcGEj4KSUR8v8tMtCZkrla_f0OHcoOE_y3wR-ooh0eugXGB_v8RkElEHR8X2arwZLJr-j6zrf93s_9XBv7Rxsc_9CuVbe/s1600/SJantzen-razor_Week4_01_crop.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhPrNjy39CxU8i-OJTsEo0fzTBCZEkGrdcLX_wKbDP7B0lzCkiBcGEj4KSUR8v8tMtCZkrla_f0OHcoOE_y3wR-ooh0eugXGB_v8RkElEHR8X2arwZLJr-j6zrf93s_9XBv7Rxsc_9CuVbe/s400/SJantzen-razor_Week4_01_crop.jpg" width="387" /></a></div>
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The second part of the assignment was to explore video and to create a short (< 1 min) recording of a process. Since I've been having fun with my macro lens, I decided to use the video functionality on my Canon T2i to capture the "process". I think the video should speak for itself.<br />
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<iframe allowfullscreen="" frameborder="0" height="360" mozallowfullscreen="" src="https://player.vimeo.com/video/133923361?color=ffffff" webkitallowfullscreen="" width="640"></iframe><br />
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And the obligatory setup snap. Yes, that's a plastic horse (pegasys [sic]) with a flashlight taped to it.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjErIn5o8_18XcH3DYcbkjedQQYra6O1lHCo5DLrjZZkYk9j9mwWfdv44A1gO1zaTfj-hlUeRb0jgg9riamo0tgAYFaLUoYkOZKZiYxkdoE1WOaXeo5QZC8p4TYhS1JDq1kkZ96dRrLlCTc/s1600/IMG_20150719_151610646.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="358" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjErIn5o8_18XcH3DYcbkjedQQYra6O1lHCo5DLrjZZkYk9j9mwWfdv44A1gO1zaTfj-hlUeRb0jgg9riamo0tgAYFaLUoYkOZKZiYxkdoE1WOaXeo5QZC8p4TYhS1JDq1kkZ96dRrLlCTc/s640/IMG_20150719_151610646.jpg" width="640" /></a></div>
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Thank you for reading and watching!<br />
Stuart<!--1-->Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-58813951070348522732015-07-19T17:26:00.001-04:002015-07-19T17:26:47.409-04:00Maya Course - 10 videos so farSo far I've uploaded 10 videos from the Maya course I taught this spring. If you're interested in learning a variety of Maya topics, I highly recommend <a href="https://www.youtube.com/subscription_center?add_user=biocinematics" target="_blank">subscribing</a> as I upload the remainder of the course. A few selected vids:<br />
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A shorter segment on animating cameras in Maya
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/3n-DuieAI3o?rel=0" width="640"></iframe>
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A fun overview of how driven keys can be helpful in rigging
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/ixvp_7-GpEQ?rel=0" width="640"></iframe>
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And an introduction to the MEL scripting language
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/gKrXSZkjRSk?rel=0" width="640"></iframe>
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Later,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-65691019311812690452015-07-14T09:08:00.000-04:002015-07-14T09:08:59.527-04:00Science Photography EdX Course - Week 3<div class="separator" style="clear: both; text-align: left;">
Week 3 of the science photography course has come and gone, and the assignment this time was about different lights and light positioning.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUY6xD2F15k5RTImm1fqJMsuCuKEzZuE72UNRQO-yP24PGz2K1VOHL8I91RfzBQeY_0IdiFRZ6hIQYaugxsMJ3Er-XYPEXVagAFFcycjLRCl-PfVo9rAu-or6btpJCQ-Caaoh_qa6RtFpf/s1600/SJantzen-20150713_Week3_01.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="426" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUY6xD2F15k5RTImm1fqJMsuCuKEzZuE72UNRQO-yP24PGz2K1VOHL8I91RfzBQeY_0IdiFRZ6hIQYaugxsMJ3Er-XYPEXVagAFFcycjLRCl-PfVo9rAu-or6btpJCQ-Caaoh_qa6RtFpf/s640/SJantzen-20150713_Week3_01.jpg" width="640" /></a></div>
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I started out with some limited daylight from the front. There is a bit of a gleam, but fairly uninteresting in terms of light.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdAfVjmBQVSN_8AtqS23HordcuZNBWhcf_uG-JyzGNHj4gdnMFHYocfHKC4twL0Og1r7Nakjj3NmuvL5PNVFr7Pw89Myx6NUMdUt6k7SPneeszc7pZigouehK1ZRh7TZ3qv4Hj1TIh2NyX/s1600/SJantzen-20150713_Week3_02.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="426" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdAfVjmBQVSN_8AtqS23HordcuZNBWhcf_uG-JyzGNHj4gdnMFHYocfHKC4twL0Og1r7Nakjj3NmuvL5PNVFr7Pw89Myx6NUMdUt6k7SPneeszc7pZigouehK1ZRh7TZ3qv4Hj1TIh2NyX/s640/SJantzen-20150713_Week3_02.jpg" width="640" /></a></div>
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Then I added another light, in the above image it is bouncing off an umbrella from the front right. Still pretty similar to the daylight only, just mainly some color differences. Below you can see the setup I was using for these initial photos.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiny2GbvTOEHti1Y84hyphenhyphenk0FBJvAZpYQmvamX2TUNBLQn3zi_SDANfMormabcxHOtHah5WgYzatugSlypMFpwIAcqdh5TcDCbapI_HlQ6TyBsh6DqPO6BvVxDP6PKxcWRUb-EBi9TffvGvIP/s1600/SJantzen-20150713_Week3_04.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="426" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiny2GbvTOEHti1Y84hyphenhyphenk0FBJvAZpYQmvamX2TUNBLQn3zi_SDANfMormabcxHOtHah5WgYzatugSlypMFpwIAcqdh5TcDCbapI_HlQ6TyBsh6DqPO6BvVxDP6PKxcWRUb-EBi9TffvGvIP/s640/SJantzen-20150713_Week3_04.jpg" width="640" /></a></div>
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Then I tried the bare light (without the umbrella bounce) and I think this is much more interesting. The watch interior has more of a gleam to it.<br />
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This series really demonstrates how drastic an effect simply changing the light position can have. I hope I have the descriptions correct; it was a bit hard to remember exactly where the bulb was in each. Check if my analysis makes sense.<br />
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It was very interesting how a low light (the bulb was just an inch or two from the watch and my lens) casts the etching/engraving in sharp contrast and gives a graininess to the flat surfaces.<br />
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Whereas a higher light makes things appear more glossy with lots of specular highlights.<br />
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This final one might be my favorite from the shoot, in terms of composition and lighting.<br />
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Later,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-22359924621212166422015-07-04T17:38:00.000-04:002015-07-04T17:38:20.048-04:00Science Photography EdX Course - Week 2Week 2 of my EdX Science Photography Course involved an exploration of aperture and depth of field. Here are three images from the series. Not a tremendous difference between them, but I think you can get the idea of the depth of field changing.<br />
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Does it bother you that the f and 1 aren't visually aligned? I suppose it does now. I should have noticed that and tweaked it.<br />
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To create the images, I decided to build a DIY lightbox out of a cardboard box, parchment paper, white duct tape, and some sticky drawer liner and printer paper.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1Qyh_VEXA2KA_syJWfxbjt1DBEVjHRWYkfeAdbsqWgY7oOIxQ-eX3RrlEb9lhaflVw8QQX7qA1ZKC-KrkxFurDkcp1ZLWvqcT_hTUBlwQy37c0R6CbmlXkePvbfWEhg_BNHO5ArgJyiZt/s1600/IMG_20150701_155637620.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="223" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1Qyh_VEXA2KA_syJWfxbjt1DBEVjHRWYkfeAdbsqWgY7oOIxQ-eX3RrlEb9lhaflVw8QQX7qA1ZKC-KrkxFurDkcp1ZLWvqcT_hTUBlwQy37c0R6CbmlXkePvbfWEhg_BNHO5ArgJyiZt/s400/IMG_20150701_155637620.jpg" width="400" /></a></div>
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Then using my cheap studio lights, I was able to flood the interior of the box with nice diffuse light. I look forward to using the box in some other projects too. I'm using my Canon Rebel T2i and 100mm f/2.8 Macro here.<br />
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Later,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-1140581556855791972015-06-30T20:51:00.000-04:002015-06-30T20:53:09.401-04:00Maya Course - Lectures on YouTubeToday I uploaded the first three lecture chunks (for lack of a better word) of the course I taught this spring on <a href="https://www.youtube.com/user/biocinematics/videos" target="_blank">YouTube</a> free for anyone to watch.<br />
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<iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/0Q_jfIjxa4A?rel=0" width="640"></iframe>
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The course was offered through the <a href="http://bmc.med.utoronto.ca/bmc/" target="_blank">Masters of Science in Biomedical Communications program</a>, the Master's program that I completed two years ago. It covers intermediate and advanced Maya topics, or more specifically, pretty much everything that isn't modelling and texturing.<br />
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The recorded lectures are largely Maya demonstrations, tutorials, and explanations that focus on the application of a Maya toolset or technique for biomedical content. Admittedly some of the demos are less biomedical and more "let's use some spheres because it's simpler to demonstrate". They assume some prior knowledge of Maya and a decent understanding of the interface and modelling tools.<br />
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Lecture topics (that I will be posting regularly) include Animation, Rigging, nParticles, Optimization, nHair, nCloth, Fluids, Motion Tracking and Compositing with AE, and MEL scripting. I very much hope that you will <a href="http://www.youtube.com/subscription_center?add_user=biocinematics" target="_blank">subscribe</a> to my <a href="https://www.youtube.com/user/biocinematics" target="_blank">YouTube channel</a> to view the tutorials as soon as they are posted. There will be 35 videos of varying lengths in the series, so lots of content to come.<br />
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Thanks for checking them out! I hope they are informative and useful, and if so, please share them around.<br />
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Later,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-27090051090790038352015-06-28T21:35:00.001-04:002015-06-29T09:28:18.511-04:00Science Photography EdX Course - Week 1I registered for a <a href="https://courses.edx.org/courses/course-v1:MITx+0.111x+2T2015/info" target="_blank">Science and Engineering Photography course offered by EdX</a> since I am quite interested in science and nature photography, I've just purchased a macro lens, and I really like the work the instructor has done. Today I completed the first assignment. I will be working with the same object for the duration of the course, so it was important that I choose something interesting and had some significance to me. Fortunately my good wife thought to suggest my great-grandfather's pocket watch, which I inherited after he passed away several years ago at the age of 102. This wasn't his Watch (with a capital W) in the sense of it being <i>the</i> heirloom, since he had several watches and was more of a wrist-watch type of guy, but it still has plenty of significance for me and looking at it now, it could be as old as late 19th century though more likely c. 1930-50. Perhaps I'll be able to discover exactly when it was made while doing this course.<br />
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The first assignment was not to use a camera, rather a flatbed scanner. This ended up being a very interesting technique and something I hope to return to in the future. My scanner is capable of scanning at up to 12800 dpi, so ended up with some very large images. A bit overkill, but here is a very scaled down image.<br />
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Aside from creating some nice images of the watch face, I stumbled on a pretty surprising effect. Look at the second hand (the inset dial). What is happening here? All the evidence is already in the image, but I'll give a couple of clues. 1) The watch still works 2) The scanner head moves from the top of the image to the bottom. Let me know your analysis in the comments.<br />
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And finally, because my artist sister-in-law was over, she noticed the cool moving second hand effect and asked what would happen if I moved the whole watch during the scan. A scan and a bit of photoshop processing later (though not as much as you might expect for this image), I arrived at the below photo.<br />
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I just love the swirly chromatic strands on the hour and minute hands.</div>
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This course, while very exciting and about which I will be posting frequently, is not the special announcement I was going to make, so stay tuned again for the actual announcement.</div>
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Later,</div>
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Stuart</div>
<br />Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-57507342048436815402015-06-27T14:18:00.001-04:002019-02-28T14:50:32.910-05:00Molecular Visualization Principles #1-3As a part of my research work, we are developing some principles, guidelines, or considerations for visualizing molecules in biological systems. It's hard to know exactly how to phrase and frame these, because they are not hard and fast rules; however, they may be helpful in creating more accurate depictions of biomolecules.<br />
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Each principle is presented as a short pair of animations. The Treatment A's do not adhere to the principle whereas the Treatment B's do. So far, I have created examples to demonstrate three of the principles, with more coming.<br />
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Principle 01 is "Leave some behind". It conveys the idea that typically not all molecules are consumed in a process. For example, there may be more subunits present in the environment than ultimately bind together in a biological complex. This example shows a virus capsid assembling. Note that many of the actual mechanics of capsid assembly (i.e. ideas that may constitute other principles) are ignored or simplified for the sake of clarity. One might declare some irony or hypocrisy here, however it is important that we build the framework for the principles individually before considering how they might be combined in real-world visualization cases.<br />
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Principle 02 is "Use Random Walks". It conveys the idea that molecules move randomly due to collisions in a crowded environment. For example, an Arp2/3 complex moves erratically before binding to an actin filament.<br />
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Principle 03 is "Add Non-binding Collisions". It conveys the idea that molecules might encounter each other with unproductive orientations and conformations multiple times before a successful binding event occurs. For example, Sos and Ras might collide a number of times before their orientations result in tight binding.<br />
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I'll be announcing an exciting new set of content very soon, so check back in a couple of days for that.<br />
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Later,<br />
Stuart<br />
<br />Stuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-79756323941391128542015-05-30T13:35:00.000-04:002015-05-30T13:35:35.292-04:00Molecular shadingFinally some biomedical visualization, right? These images are work in progress for a few animations I am working on to demonstrate in a simple way some important concepts of molecular behaviour. This is from my work, as opposed to a personal project.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpz7EIwK7obLoHKWP1aAQpYelU2_jFMHZC4ZR-wukYSmvQU7A75teTtGcBpyYYD2QBg1lhRr_wJ6zaKjhlBIe-DhyhbChTMj6vgbq954UgpCIY-lJ45U0NUJ_YoTZAiVKulf0t48bqutyL/s1600/p03_comp_v3_BCM.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpz7EIwK7obLoHKWP1aAQpYelU2_jFMHZC4ZR-wukYSmvQU7A75teTtGcBpyYYD2QBg1lhRr_wJ6zaKjhlBIe-DhyhbChTMj6vgbq954UgpCIY-lJ45U0NUJ_YoTZAiVKulf0t48bqutyL/s640/p03_comp_v3_BCM.jpg" width="640" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2gxLwGSiQAE6vHMcYP6iyg0_kGS-bwhpvxFB0yEEUFKAMxINvaOQ7KamEuBxWOB6Ft9gQ7wk4fuP8SBv45tAi3T_X6W8QwAnhWaiNSly6EkWfXgM-pWY1wddOBdIiT-TQEfh115AekvjG/s1600/p02_comp_03_BCM.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2gxLwGSiQAE6vHMcYP6iyg0_kGS-bwhpvxFB0yEEUFKAMxINvaOQ7KamEuBxWOB6Ft9gQ7wk4fuP8SBv45tAi3T_X6W8QwAnhWaiNSly6EkWfXgM-pWY1wddOBdIiT-TQEfh115AekvjG/s640/p02_comp_03_BCM.jpg" width="640" /></a></div>
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When creating the molecular shaders, I had two important ideas to consider. The first was that the form of the individual molecules was not very important. They should be treated simply and cleanly. I considered going as far as flat shading or toon shading, but decided against it in favor of a softer representation with a slight indication of form.<br />
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The second was that contact between molecules and their spatial relationship should be clear. Ambient occlusion is a great candidate for this, but I didn't want the AO to show form within the molecule, so I resolved this dilemma using an miLabel attribute on the objects, separate AO shaders on molecules, and using the idnonself attribute of the mib_amb_occlusion shader.<br />
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Finally I wanted to add just a bit of aesthetic interest to the molecules, so I gave them a slight sheen of a different color using a samplerInfo.facingRatio to ramp to lambert.color to achieve the effect. I'm rendering each of these components of the overall look in different render layers so I can play with the strengths of each.<br />
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For the lighting, I used a single very large area light with soft shadows and final gather that employed an IBL sphere mapped with a colored ramp. See if you can figure out the ramp colors.<br />
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Later,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-4721275551942338672015-05-22T19:31:00.000-04:002015-05-22T19:34:48.694-04:00SaD - Special PreviewLast week I released my novel <a href="http://www.amazon.com/dp/B00XS2Y6QQ" target="_blank">Severing a Dendrite</a>. Amazon provides a short sample of the book you can read before buying. However, I want to share the opportunity to read a longer section, five chapters (over 50 pages in the pdf), before potentially buying the book. Here are a few different formats for your reading pleasure.<br />
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<span style="text-align: start;">The Special Preview in PDF</span></div>
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<a href="https://goo.gl/b8swYy" target="_blank"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhn0JbuT0IaNGX8MOPeoAORC2Z9ZB-KekxKsoQvc0ehKgB81NECX3uDbe44mdWh-qy6Cn2du41KktmFLGUglpgj975IE6DNN8DgiZxfsBCMz7HZ6tSnHXbg8waHmyOmBEDbKPSifFA7YFUw/s200/SaD_Cover_sample_thumb_pdf.jpg" width="133" /></a></div>
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The Special Preview in MOBI (Kindle format; use <a href="http://www.amazon.com/gp/sendtokindle" target="_blank">Send to Kindle</a>)</div>
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<a href="https://goo.gl/USDZry" target="_blank"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRcagEQTHN68tvdHtCxed6H8X-loAUtqKq0EbTuJ4gpt5NaT2PRMccl7MbCBkGtXrC-rhJ6ODRS5IPVlByXvjSku9TD-jfG2qZdjPwWmcFrSMqjJH3EVg5nTzmuWcdWppv_AmCbRnPSECS/s200/SaD_Cover_sample_thumb_mobi.jpg" width="133" /></a></div>
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<span style="text-align: start;">The Special Preview in EPUB (other eReaders)</span></div>
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<a href="https://goo.gl/zok0a8" target="_blank"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1XD4b2xp6vTnmHeiidxBBzY7sLH3UD-NjKLQgEZqjMlKZiggmU6u4FejSnn6rzR1adLgLZxFfWk-95jMDrYCuWRa8Vk6BfMZM6FFPp2WFNkR2NV6XrdvlR-zMyW_Gb-81qIMVFH3P8rXf/s200/SaD_Cover_sample_thumb_epub.jpg" width="133" /></a></div>
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If you are wanting to read these previews on a device (or buy the Amazon book), and aren't sure if it will work or how to go about it, send me an email (stuart@biocinematics.com) and I will help out as best I can.<br />
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If you are a non-kindle user and you <i>really </i>want the whole book in EPUB format, shoot me an email (stuart@biocinematics.com) with a screenshot of your amazon receipt and I'll hook you up with an EPUB file.<br />
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Thank you so much to everyone that has purchased the book so far. Of much greater importance than the two bucks I receive, I'm thrilled that someone is reading the story I wrote, and I'm very curious to hear what people think. If you've read all or part of it, I would love a) an amazon review, b) a comment below with your thoughts, or c) an email with your honest opinion.<br />
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Thanks again,<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0tag:blogger.com,1999:blog-197012358288299042.post-54147184596682881472015-05-18T18:37:00.001-04:002015-05-18T18:37:09.054-04:00SaD - About the CoverI released my first novel two days ago (http://www.amazon.com/dp/B00XS2Y6QQ) and interestingly, the cover was one of the most challenging parts (see <a href="http://biocinematics.blogspot.ca/2015/05/severing-dendrite-now-available.html" target="_blank">the previous pos</a>t for a nice look at the cover). I played around with a couple of 2D geometric/graphical ideas and then discarded those in favor of a 3D recreation of one of the characters from the book.<br />
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The book is full of plants and animals similar yet dissimilar to those we are currently surrounded by. I wanted to capture a bit of mystery, a bit of familiarity, and a bit of softness and appealing texture. An image came to mind of an animal with a long curved tail, a back, and ears visible almost in silhouette. Perhaps someone else has done this and I subconsciously borrowed the idea, but I think it suits the feel of the novel. If you read the book, you'll know who the character is (<promo> buy it </promo>).<br />
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ZBrush is a great tool for messing around with ideas in digital clay, and dynamesh allows you to work without worrying about edge flow, poly counts, or anything technical.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW8K2TeYlrcL8CTf3bUSGotTx0ogQIRHj2llEsg-3TPlJrwts0Us669ddwy_9DkS2dM4jO4J6X5TO-nccOBPSMjM87LC4Blqr9u8jSZkxukhXVo_M8MKh6Kk-aw73ooqBdRrAYT_DRwqJv/s1600/ZBrush_cover_BCM.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="262" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW8K2TeYlrcL8CTf3bUSGotTx0ogQIRHj2llEsg-3TPlJrwts0Us669ddwy_9DkS2dM4jO4J6X5TO-nccOBPSMjM87LC4Blqr9u8jSZkxukhXVo_M8MKh6Kk-aw73ooqBdRrAYT_DRwqJv/s640/ZBrush_cover_BCM.jpg" width="640" /></a></div>
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I sculpted out what I thought the hairless version should look like (left), then drew guides for the automatic retopology process (middle) after which I got a decent medium resolution mesh to work with in Maya (right).<br />
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I also painted a rough texture on the model in ZBrush, allowing it to be pretty loose and non-photorealistic because it would sit under the fur. It would also define the fur color. Then I unwrapped the UVs and exported the texture to photoshop.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju1NzdM_DcRz8V1sS_XDszbbib6d3VWJF5j670TtxDPFouyRcS5BuaYhdrEZhQmnXJf-L3ciFcwtCBz3HYwHtsQGqJJs1BELnwfeR_PuYPA64bH6vZktMToB6KUwrgWKnwAQUFFnBboUV3/s1600/PS_texture_BCM.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju1NzdM_DcRz8V1sS_XDszbbib6d3VWJF5j670TtxDPFouyRcS5BuaYhdrEZhQmnXJf-L3ciFcwtCBz3HYwHtsQGqJJs1BELnwfeR_PuYPA64bH6vZktMToB6KUwrgWKnwAQUFFnBboUV3/s400/PS_texture_BCM.jpg" width="400" /></a></div>
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I brought the model into Maya, connected the diffuse texture and set up the camera to match my working illustrator layout.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgycO0SvBrTEqdX8SuDA7cOSJEQobwjL4p6MIUctZcKmdigMe3qSZCMLT7jRPLSEVjiZ_fl4fAify9ykmINT_ZMkqutUdiI8UspeX4OtpfXLjPYnpErmR3zbgD1DwSAy5duQy4gXvHryHWs/s1600/Maya_framing_BCM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="286" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgycO0SvBrTEqdX8SuDA7cOSJEQobwjL4p6MIUctZcKmdigMe3qSZCMLT7jRPLSEVjiZ_fl4fAify9ykmINT_ZMkqutUdiI8UspeX4OtpfXLjPYnpErmR3zbgD1DwSAy5duQy4gXvHryHWs/s400/Maya_framing_BCM.png" width="400" /></a></div>
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In order to get the fur on the animal, I had two options in Maya: xgen or the classic fur system. I tried working with xgen, because it is supposed to be the new workflow for fur, hair, and arbitrarily generated primitives (their words). Unfortunately it got the better of me, and I couldn't get colored workable fur. That was the point where I didn't get my cover out and published, and so began the move, the baby, and temporarily putting the project on hold.<br />
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More recently I returned to the project and began working with the classic fur system. One might expect that I started with the Racoon preset, but I actually started with the Calico Cat fur preset and did all the tweaks and changes from there.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAfBlx3OD7T94RSTMr6zKlPLsNnPRdeN0qU5_h-ddMdVazU-P_AEKwigN_ujWBSrKF0o6pyklYOKMiXfzqSE7-MM8vWg_YLG7yEO-pOukH2TDRNpbFtCrPFenNiLUss0X21ZMkAP_NHuQR/s1600/Calico_cat_preset.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAfBlx3OD7T94RSTMr6zKlPLsNnPRdeN0qU5_h-ddMdVazU-P_AEKwigN_ujWBSrKF0o6pyklYOKMiXfzqSE7-MM8vWg_YLG7yEO-pOukH2TDRNpbFtCrPFenNiLUss0X21ZMkAP_NHuQR/s1600/Calico_cat_preset.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Maya Fur Preset: Calico Cat</td></tr>
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In photoshop, I made modified copies of the diffuse texture to be used as the fur base color, the fur tip color, as well as various grayscale maps to drive properties of the fur itself (length, baldness, bending).<br />
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The ears were the most frustrating part, and I created a whole separate fur system just for the rims of the ears. This meant painting even more grayscale maps, but I still found it more intuitive to work with than xgen.<br />
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<tr><td class="tr-caption" style="text-align: center;">Looks pretty ugly until render time</td></tr>
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In terms of lighting, I thought I would need something sophisticated and clever to highlight the fur, but it turns out I was quite happy with a pretty standard Physical Sun and Sky setup, though I made sure to turn off the automatic gamma correction (Linear Workflow all the way).</div>
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Once rendered, I did some post-processing in Photoshop. I performed color correction, cleaned up some of the fur manually, added a slight warm back-lit glow to the ear, and made a few other tweaks. Then I assembled it with the text in Illustrator. I used Playfair Display as the typeface and tried to keep the composition nice and simple.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrcLy-Z640fAgMBRCzMKpeirFcGIoEUKqI22A7cbee2GLTY3PwARhLhxYCLomHTAMo3YfbPFYOj6bHUS3N1IAk8LriohsUIQNqt_B6zXGzSmrLCgJMNHrq-3Dx5kFX6ICOGDPY3RzPdS45/s1600/Illustrator_comp_BCM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrcLy-Z640fAgMBRCzMKpeirFcGIoEUKqI22A7cbee2GLTY3PwARhLhxYCLomHTAMo3YfbPFYOj6bHUS3N1IAk8LriohsUIQNqt_B6zXGzSmrLCgJMNHrq-3Dx5kFX6ICOGDPY3RzPdS45/s640/Illustrator_comp_BCM.png" width="466" /></a></div>
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Along the way, I made sure it looked good in grayscale, since many kindle readers are black and white (I mean the devices, not the people...). And that's pretty much it! Oh yeah... nudge: <a href="http://www.amazon.com/dp/B00XS2Y6QQ">http://www.amazon.com/dp/B00XS2Y6QQ</a><br />
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Later!<br />
StuartStuarthttp://www.blogger.com/profile/14439928627377421130noreply@blogger.com0