tag:blogger.com,1999:blog-13823291141495655422024-03-06T03:51:24.698+00:00Calculated ImagesFrom experimental art, photography and image generation to microscopy and science by Richard Wheeler.
I run a research lab in the University of Oxford, with a focus on parasite cell biology, microscopes, and computational analysis.Unknownnoreply@blogger.comBlogger113125tag:blogger.com,1999:blog-1382329114149565542.post-32665928475297510582021-05-25T19:01:00.004+01:002021-05-26T13:26:04.488+01:00Trypanosomatid cell structures<p></p><div class="separator" style="clear: both; text-align: left;"><div class="separator" style="clear: both;">These are my oft-requested diagrams of trypanosomatid parasites. They're heavily inspired by the amazing illustrations of trypanosomatids by <a href="https://pubmed.ncbi.nlm.nih.gov/27631276/">Keith Vickerman</a>, like <a href="https://pubmed.ncbi.nlm.nih.gov/3928017/">this classic</a>, though with a more modern twist.</div><div class="separator" style="clear: both;"><br /></div><div class="separator" style="clear: both;">Both aim to be fully accurate diagrams, targeting a specialist text book or review paper level. They're drawn based on on lots of papers, both by others and by me, plus many hours on electron microscopes looking at them! They are slightly 'cartoony' though, exaggerating the size of some of the organelles/structures for clarity.</div></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhP5iYnSzYGN5ICgLEUZIRyVSbtUDVV0D_CqV5tCI-zls78n_hTIkvljYueYFvCzs23UmFEWZfP00LKjtGpiu8X-R4-rrAQts5dW-X30gptnGaloOe4w5wM6o7-A6AE2ICiaG8xjXWweA/s2048/Trypanosome.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1448" data-original-width="2048" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhP5iYnSzYGN5ICgLEUZIRyVSbtUDVV0D_CqV5tCI-zls78n_hTIkvljYueYFvCzs23UmFEWZfP00LKjtGpiu8X-R4-rrAQts5dW-X30gptnGaloOe4w5wM6o7-A6AE2ICiaG8xjXWweA/s320/Trypanosome.jpg" width="320" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div></div><div class="separator" style="clear: both; text-align: center;"><i>Trypanosoma brucei </i>procyclic trypomastigote form - as found in the tsetse fly midgut. This diagram is featured in my annual review with Keith Gull and Jack Sunter: <a href="https://www.annualreviews.org/doi/10.1146/annurev-micro-020518-115617">Coordination of the Cell Cycle in Trypanosomes</a></div><br /><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhPqnECz4U3cZC1DKtV8oMpfdbF6kEiyNz8EXG5zB7ZfVzNmUDE_G7OUYplByWrG0GY8CMN6tkxWRU6SqZsUeoV99tZd1nlDiP7e82IOCN-mkSfpNP7CFAs5V9c1Oizy72_eZ_scsLyu-Y/s2048/Leishmania.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1448" data-original-width="2048" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhPqnECz4U3cZC1DKtV8oMpfdbF6kEiyNz8EXG5zB7ZfVzNmUDE_G7OUYplByWrG0GY8CMN6tkxWRU6SqZsUeoV99tZd1nlDiP7e82IOCN-mkSfpNP7CFAs5V9c1Oizy72_eZ_scsLyu-Y/s320/Leishmania.jpg" width="320" /></a></div><div class="separator" style="clear: both; text-align: center;"><i style="text-align: left;">Leishmania mexicana </i><span style="text-align: left;">procyclic promastigote form - as found in the sandfly midgut. Drawn in the same style as </span><i style="text-align: left;">T. brucei</i><span style="text-align: left;">, but not published.</span></div></div><br />Trypanosomatid parasites are wonderfully structured and intrinsically beautiful cells. They've been the subject of many of my illustrations over the years, you'll find them around, and give a track record of my illustration skill... for better or for worse.<div><br /></div><div>Please ask before using these - they represent a big investment of time - but they are made to be used and belong in lecture slides! Drop me a message if you need really high resolution versions, vector versions (pdf/svg), etc.</div>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-68276450080401907352019-10-15T12:09:00.001+01:002019-10-15T12:09:58.227+01:00Tryp/Leish Stickers!<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWKJ9nP3F9L1UsRiNjYY9xbxbSyL6_kUExnQXbfx-ljA3xkS_MT8MjISIF1_QK19CFZu6KTwRzcHMxeqgi1yoLzaxz_VRjttN8IZyXTGyZ4rdh01M2OVfLtvGZB_M2UMwLHU4RwNVpN68/s1600/TrypStickers_1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWKJ9nP3F9L1UsRiNjYY9xbxbSyL6_kUExnQXbfx-ljA3xkS_MT8MjISIF1_QK19CFZu6KTwRzcHMxeqgi1yoLzaxz_VRjttN8IZyXTGyZ4rdh01M2OVfLtvGZB_M2UMwLHU4RwNVpN68/s640/TrypStickers_1.jpg" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
It's been a busy year starting my lab... But in more important news, <i>T. brucei, T. cruzi </i>and <i>Leishmania </i>stickers!</div>
<br />Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-58305429370586284832018-09-18T10:02:00.002+01:002018-09-18T16:03:07.467+01:00How does a cell swim fowards?<div class="MsoNormal" style="text-align: left;">
“Why are they swimming backwards?” This is one of the most common questions I get asked whenever I show a video of <i>Leishmania </i>parasites swimming.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5XzTRluczuZNoapRhbjHXyRwQUbFZnkxWSL6ealBheO3UmtGiSdM-MGMu4YlR3DbFdjbVw2rCtkcqMD5aof6P__8qWYb2VO9QIKy1xsKCrBfJbQLqaimoT1VailZwsd8HNQQJXk8ePfg/s1600/LeishSwimming_1_8bit.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5XzTRluczuZNoapRhbjHXyRwQUbFZnkxWSL6ealBheO3UmtGiSdM-MGMu4YlR3DbFdjbVw2rCtkcqMD5aof6P__8qWYb2VO9QIKy1xsKCrBfJbQLqaimoT1VailZwsd8HNQQJXk8ePfg/s320/LeishSwimming_1_8bit.gif" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: x-small;">Swimming <i>Leishmania</i> at 200 frames per second (8× slower than actual speed)</span></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
If you look at <i>Leishmana </i>with a high speed video it's easy to see they tend to swim 'tail-first', with the flagellum sticking forward into the direction of travel. Sperm, probably the best-known swimming cells, do the opposite, and swim 'head-first'.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
</div>
<div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAjgYps5NW_8CPvWQ_5Mk6UPY1Hji5K5QdloQ6hapXM7TdSfyNdXHymaScwjOmONSbaC22nZxK9snjfwCn9B7mMZYH04GhCq7sqg1LyGShq7WZop-qwP7MIXzNNZCQzwXkXSS69MVOn0g/s1600/Sperm.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="183" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAjgYps5NW_8CPvWQ_5Mk6UPY1Hji5K5QdloQ6hapXM7TdSfyNdXHymaScwjOmONSbaC22nZxK9snjfwCn9B7mMZYH04GhCq7sqg1LyGShq7WZop-qwP7MIXzNNZCQzwXkXSS69MVOn0g/s200/Sperm.png" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5_wE6Kthae3ZHlPLdzNfiQObe_5OdcaEfXoReVvhRnxFhdvrsQrI9y-Q9UYCWjbBPYbZaMERsMjW3vHYvXvsTpHc_N5PFBfsdNMjcL9W5RXrH0waAoNmw1UUkQmLpQpzC4r3Dvb8mdEs/s1600/Leish.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="184" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5_wE6Kthae3ZHlPLdzNfiQObe_5OdcaEfXoReVvhRnxFhdvrsQrI9y-Q9UYCWjbBPYbZaMERsMjW3vHYvXvsTpHc_N5PFBfsdNMjcL9W5RXrH0waAoNmw1UUkQmLpQpzC4r3Dvb8mdEs/s200/Leish.png" width="200" /></a></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Sperm on the left, <i>Leishmania </i>on the right</span></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: left;">
Of course, if you could ask the <i>Leishmania</i>, they'd say that they're swimming forwards and it's the sperm which are swimming backwards. This raises the question of how does a swimming cell decide which direction it should swim? Which direction is forwards?</div>
<div style="text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
The direction a cell swims depends on the waves which travel down the flagellum. If they start at the base and go towards the tip then the cell will swim head-first. If they start at the tip and go towards the base then the cell will swim tail tail first. So how do they choose where the waves start?</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
We answered this question taking advantage of a useful behaviour of <i>Leishmania.</i> If you look closely at the video above you can see one cell is swimming forwards (the cell on the left) and the other is turning on the spot (the cell on the right). And if you look very closely you'll see that the waves in the cell on the left start at the flagellum tip, and the waves in the cell on the right start at the base of the flagellum.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5_wE6Kthae3ZHlPLdzNfiQObe_5OdcaEfXoReVvhRnxFhdvrsQrI9y-Q9UYCWjbBPYbZaMERsMjW3vHYvXvsTpHc_N5PFBfsdNMjcL9W5RXrH0waAoNmw1UUkQmLpQpzC4r3Dvb8mdEs/s1600/Leish.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-right: 1em; text-align: center;"><img border="0" height="184" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5_wE6Kthae3ZHlPLdzNfiQObe_5OdcaEfXoReVvhRnxFhdvrsQrI9y-Q9UYCWjbBPYbZaMERsMjW3vHYvXvsTpHc_N5PFBfsdNMjcL9W5RXrH0waAoNmw1UUkQmLpQpzC4r3Dvb8mdEs/s200/Leish.png" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjVrqw03Vsegh-kqNf4Z2mw3DW2UFC-9TqG8kMmc2bSGJdqs4uLNgngT_idZrVJtJMUqxreMcca8hJA9dU2be2iOTxlGyjxU5wAJTUeoeKgN-phlpG9uJ5VPnXV6Olr80z5zlioHj_Pyf8/s1600/Leish2.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjVrqw03Vsegh-kqNf4Z2mw3DW2UFC-9TqG8kMmc2bSGJdqs4uLNgngT_idZrVJtJMUqxreMcca8hJA9dU2be2iOTxlGyjxU5wAJTUeoeKgN-phlpG9uJ5VPnXV6Olr80z5zlioHj_Pyf8/s200/Leish2.png" width="181" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: x-small;">Tip-to-base on the left and base-to-tip on the right.</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: x-small;"><br /></span></div>
<div class="separator" style="clear: both; text-align: left;">
This let us use genetic tools to try to break one direction of flagellum wave without affecting the other and tease apart how the flagellum movement might be chosen by the cell. To cut a long story short, we found differences in the motor proteins between the base and tip which seem responsible. Interestingly, similar differences turn up in many organisms, including human sperm, suggesting it might be a general pmechanism. You can read all about this in our recent paper: <a href="http://www.pnas.org/content/115/31/E7341">At the PNAS website</a> or <a href="http://wheelerlab.net/publications/30030284.pdf">as a PDF</a>.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
<a href="doi:10.1073/pnas.1805827115">https://doi:10.1073/pnas.1805827115</a></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-36335303713220404872018-09-14T14:43:00.002+01:002018-09-14T14:43:29.784+01:00How happy are your HeLa cells?<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeQLLOyvrURAojTqNU7YRGr0OAbZ3nfU1Sn407V9NwNUWPiyvSrX90zjEoTBoW41gSV8zXJDViDahfT5b8uxp0zxEcwwHYI8ktCRWYKwf2cOjACIOr6LIY3A-WEJDym-JtK7lf0pGD_KI/s1600/HeLaHappinessScale.jpg" imageanchor="1"><img border="0" height="452" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeQLLOyvrURAojTqNU7YRGr0OAbZ3nfU1Sn407V9NwNUWPiyvSrX90zjEoTBoW41gSV8zXJDViDahfT5b8uxp0zxEcwwHYI8ktCRWYKwf2cOjACIOr6LIY3A-WEJDym-JtK7lf0pGD_KI/s640/HeLaHappinessScale.jpg" width="640" /></a><div>
<b>Figure 1. HeLa cell nucleus happiness scale. </b>HeLa cells expressing FUS eGFP were asked how they felt. The morphology of the nucleus and nucleolus, visible via FUS eGFP localisation, was used to infer happiness. The response was ranked by two independent experts, and used to build a HeLa happiness scale.</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-16888830421807026272018-05-01T22:36:00.000+01:002018-05-01T22:36:04.768+01:00Impossible Pipes<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ6mLbPw7FqudQBdrRUW-ZbhCYTVfSCgU8uMkDab8tiNhyphenhyphenKof6D6qqTGWtEb8NvcGC1e1xr5WNf5qmOenVVx7uvr84BF2s2P_U_XIIAJ4BCExccToVRo03lPYg9xznD5_VDfqDaFN5qCI/s1600/PipesIso_A1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ6mLbPw7FqudQBdrRUW-ZbhCYTVfSCgU8uMkDab8tiNhyphenhyphenKof6D6qqTGWtEb8NvcGC1e1xr5WNf5qmOenVVx7uvr84BF2s2P_U_XIIAJ4BCExccToVRo03lPYg9xznD5_VDfqDaFN5qCI/s400/PipesIso_A1.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAUY5wmCODyslN9wQNIeSKmlKxtn3wOEzE7F_2DqVGk0B-kEpzMbZDIu9F-8F2uiF3HjbLDpY8g_eMSyoFcrsjT7_S7yqMM_-8ymP3oDrQE4iyGezKz0lfHxvhAy2dh73IIP2IJGZIICg/s1600/PipesIso_A2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAUY5wmCODyslN9wQNIeSKmlKxtn3wOEzE7F_2DqVGk0B-kEpzMbZDIu9F-8F2uiF3HjbLDpY8g_eMSyoFcrsjT7_S7yqMM_-8ymP3oDrQE4iyGezKz0lfHxvhAy2dh73IIP2IJGZIICg/s400/PipesIso_A2.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEt4BoNsm_ZDVlWrBOlD63i661uijcu7B5o2eZRnbNzm6lbECrKiLbt8qPGM5jUXibvhXwWdpPUdX95YKWQXeHL8PXhdtS15eguUCkUdPWZaDgXvLY2YSa4kRqctOyrIxIxhclyGSRJO4/s1600/PipesIso_A3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEt4BoNsm_ZDVlWrBOlD63i661uijcu7B5o2eZRnbNzm6lbECrKiLbt8qPGM5jUXibvhXwWdpPUdX95YKWQXeHL8PXhdtS15eguUCkUdPWZaDgXvLY2YSa4kRqctOyrIxIxhclyGSRJO4/s400/PipesIso_A3.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEvKRmnaK8hyphenhyphenKdMj2dRLLbHOV1FTasYSyBAEiz7OLfAlPWLSxSjjvLrDtfl-3S2OPCLLOAbscItBkw2c7u-p_fqf22mEB33H6jpYTUlWikXVFgEwCtR2-q7Wz8wZpDx5KSvtJufExHkw0/s1600/PipesIso_A4.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEvKRmnaK8hyphenhyphenKdMj2dRLLbHOV1FTasYSyBAEiz7OLfAlPWLSxSjjvLrDtfl-3S2OPCLLOAbscItBkw2c7u-p_fqf22mEB33H6jpYTUlWikXVFgEwCtR2-q7Wz8wZpDx5KSvtJufExHkw0/s400/PipesIso_A4.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1ZDCmY1oQkeyPMYz5dHw5ZMxdSHjRIoUPaJlwUY1swNLTuTpEjJzw0wS4wPE45Kb8t8vIqzVTn4xbcCtrbN54tjH4PP3WNueRi4fKvy0wPKJfK25fj6oPCuduimjkUmvbUE-xlGzSFl4/s1600/PipesIso_B1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1ZDCmY1oQkeyPMYz5dHw5ZMxdSHjRIoUPaJlwUY1swNLTuTpEjJzw0wS4wPE45Kb8t8vIqzVTn4xbcCtrbN54tjH4PP3WNueRi4fKvy0wPKJfK25fj6oPCuduimjkUmvbUE-xlGzSFl4/s400/PipesIso_B1.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJytTlQYjz652oyZY_AB-9lre0ETzvzyNwwnfLM7AHGiTUPlD7egwabc2LA6OXuDkfI_gFi4gFlhp1EkDrvWhUpr8KggkOV5_lKgoIU_RblnsB6g_ZglL8p0cCpyX5rbv77lGoEOlgdss/s1600/PipesIso_B2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJytTlQYjz652oyZY_AB-9lre0ETzvzyNwwnfLM7AHGiTUPlD7egwabc2LA6OXuDkfI_gFi4gFlhp1EkDrvWhUpr8KggkOV5_lKgoIU_RblnsB6g_ZglL8p0cCpyX5rbv77lGoEOlgdss/s400/PipesIso_B2.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiICl_09HrwYNly3eMpccrAYxZdRvzdqn3KfibmoXF8pyglk5EJwC0sbZwtsXlStEkw6F2GwBxjK1WineWW00dgmomq491n0LTs4PuyRIn8TfsNvgO0iDsQErBy1FPJCmoW_DSGtSpvnzQ/s1600/PipesIso_B3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiICl_09HrwYNly3eMpccrAYxZdRvzdqn3KfibmoXF8pyglk5EJwC0sbZwtsXlStEkw6F2GwBxjK1WineWW00dgmomq491n0LTs4PuyRIn8TfsNvgO0iDsQErBy1FPJCmoW_DSGtSpvnzQ/s400/PipesIso_B3.jpg" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8lErVQg0F11QMroixaCvsR-gHh1L77rokP7LdH7krOiI1ByZ3B0-lYE_57AFcPXkC30Fn-U7UCjZMiaQMekXcwjmOCxua6N-a0acYJKn5o-fA5kcGtn7z1DzmUf-R3O5uSNeJPinn7F8/s1600/PipesIso_B4.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8lErVQg0F11QMroixaCvsR-gHh1L77rokP7LdH7krOiI1ByZ3B0-lYE_57AFcPXkC30Fn-U7UCjZMiaQMekXcwjmOCxua6N-a0acYJKn5o-fA5kcGtn7z1DzmUf-R3O5uSNeJPinn7F8/s400/PipesIso_B4.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
You can download the full set <i>via </i><a href="https://zephyris.deviantart.com/art/Impossible-Pipes-743024063">Deviantart</a></div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Software used: <a href="https://www.blender.org/">Blender</a></div>
<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-84622660466029287962017-10-30T17:21:00.002+00:002017-10-31T23:50:23.014+00:00How to be a parasiteFor an organism to become a parasite it has to adapt to live in a host. This might mean it needs to grow faster, invade cells or tissues, or avoid being killed by the immune system. It can also 'forget' how to live outside a host. It can forget how to search for food, how to survive the cold, and how to avoid drying out.<br />
<br />
We can learn how parasites adapt to infect hosts by looking at the nearest free living relatives. What had the parasite lost relative to the free living cousin, because it just doesn't need it to survive in a host? Or <i>vice versa</i>, what has it kept because it's useful for infecting a host?<br />
<br />
I've looked at this question for trypanosomatid parasites. They are protozoan (single cell) parasites, like the malaria parasite, and cause several deadly tropical diseases.<br />
<br />
A few hundreds of millions of years ago, they weren't parasites at all. The ancestors of these parasites were free living, probably swimming in ponds, lakes and seas. Then, at some point, some evolved the ability to infect insects.<br />
<br />
Millions of years passed. Then, several tens of millions of years ago, some managed to get transmitted from their host insect into a vertebrate host. And, most importantly, they survived and could get transmited back to the fly.<br />
<br />
This adaptation to infect animals probably happened on three separate occasions. Those parasites kept evolving and adapting, and are now the three human trypanosomatid-caused diseases: Sleeping sickness, Chagas disease and leishmaniasis.<br />
<br />
My most recent paper is all about this. Julius Lukeš has discovered a species of trypanosomatid that only infects insects, and looks like it hasn't changed much from the first ancestor ever to infect insects.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi14KeKZv7PdES8RfB1T4emrPa-irBvRoJmKtvfzRvmtcpwrwaHbfRnOIMMZN-iJ1KlUOu5kFfu0RiJTr4RgMi1aoTbZR5S4jGr_K0pQaHbFKi3w4jQuOR5e-BJZdIcCR5WZB2hu8djMQk/s1600/09_small.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi14KeKZv7PdES8RfB1T4emrPa-irBvRoJmKtvfzRvmtcpwrwaHbfRnOIMMZN-iJ1KlUOu5kFfu0RiJTr4RgMi1aoTbZR5S4jGr_K0pQaHbFKi3w4jQuOR5e-BJZdIcCR5WZB2hu8djMQk/s400/09_small.png" width="400" /></a></div>
<br />
<br />
With Tomáš and Eva, we looked at what this species tells us about how these parasites adapted to infect flies: How does the cell grow, adapts its shape, and stick to surfaces? How does its internal organisation adjust to allow these changes? How does its metabolism change for different energy sources? And, how has the genome, which encodes the proteins that drive these functions, changed to achieve this?<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZ5lJSeV8-zpPUJlQW9HV7ngO2SGmhcuGaCEINeUIrEHSL5APb9PZIZwb43nv0-Bd-hnH0-RXn0980eNSEN778MBRPMdFo2hmpViwiqubzDyXeHrGBAKkIjNP0UDs04EhhwrVX0mq6CeY/s1600/Paratrypanosoma-Fig.+6.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="345" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZ5lJSeV8-zpPUJlQW9HV7ngO2SGmhcuGaCEINeUIrEHSL5APb9PZIZwb43nv0-Bd-hnH0-RXn0980eNSEN778MBRPMdFo2hmpViwiqubzDyXeHrGBAKkIjNP0UDs04EhhwrVX0mq6CeY/s400/Paratrypanosoma-Fig.+6.png" width="400" /></a></div>
<br />
<br />
Using this information, we could then get insights into what is important for human infective parasites. What aspects of shape, structure and metabolism adaptations have they 'forgotten'? And which have they kept? The ones they have kept are the ones important for infecting, and killing, people.<br />
<br />
Want to read more? You can get a copy of the paper from my website: <a href="http://richardwheeler.net/contentpages/publicationgallery.php?gallery=Publications">richardwheeler.net</a><br />
<br />
Skalický T*, Dobáková E*,1, Wheeler RJ*, Tesařová M, Flegontova P, Jirsová D, Votýpkaa J, Yurchenkoa V, Ayalag FJ, Lukeš J (2017) "Extensive flagellar remodeling during the complex life cycle of Paratrypanosoma, an early-branching trypanosomatid" <i>PNAS </i><a href="https://doi.org/10.1073/pnas.1712311114">doi:10.1073/pnas.1712311114</a>Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-34231620017921914222017-02-02T20:02:00.001+00:002017-02-02T20:03:28.537+00:00Moving in a straight line - sounds simple, right?<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
One hundred years ago Asa <span style="background-color: white; color: #222222; max-height: 999999px;">Schaeffer blindfolded his friend and challenged him to walk in a straight line. He did three loops of a spiral, before tripping over a tree stump. This wasn't a cruel prank, it was an experiment, and all people are surprisingly bad at this simple challenge.</span><br />
<span style="background-color: white; color: #222222; max-height: 999999px;"><br /></span>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJGuYjtz4EFpGrh6tf8EB_hy8xPaKL-K6tSLn56SARcAGu-SJghEDdeYk4fR2c0oYkqqA12CW2Lq9Bkk6RXZ_8HcYZbdwueJZM_OnJENaTLM17WcfeZdZbgv8hIIxz5WGZMCLJGSxoRAY/s1600/Schaeffer+Spiral+w.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="292" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJGuYjtz4EFpGrh6tf8EB_hy8xPaKL-K6tSLn56SARcAGu-SJghEDdeYk4fR2c0oYkqqA12CW2Lq9Bkk6RXZ_8HcYZbdwueJZM_OnJENaTLM17WcfeZdZbgv8hIIxz5WGZMCLJGSxoRAY/s320/Schaeffer+Spiral+w.jpg" width="320" /></a></div>
<span style="background-color: white; color: #222222; max-height: 999999px;"></span><br />
<span style="background-color: white; color: #222222; max-height: 999999px;"><br /></span>
<span style="background-color: white; color: #222222; max-height: 999999px;">More modern experiments showed it is lack of external reference points that trips people up. Blindfolded in a desert? You walk in circles. Not blindfolded in a desert? Straight lines. Forest on a sunny day? Straight lines. Forest on an overcast day? Circles. </span><a href="http://dx.doi.org/10.1016/j.cub.2009.07.053"><i>Current Biology</i>, DOI: 10.1016/j.cub.2009.07.053</a></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
</div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;">People need some external reference point, a distant hill, the sun, or even the direction of shadows, to manage a straight line. Why they drift into circles without a reference isn't clear. Is it asymmetric leg strength? A handedness bias? Or some psychological miss-correction? What is clear is that it is a universal problem.</span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<br /></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;">Navigation without reference points is always difficult. This is why s</span></span><span style="background-color: white; color: #222222;">pin stabilisation is widely used to stop flying objects, from bullets to rugby balls, curving off course in the air. Even advanced tools like </span><a href="https://en.wikipedia.org/wiki/Inertial_navigation_system" style="background-color: white;">inertial navigation systems</a><span style="background-color: white; color: #222222;">, which use dead reckoning from measuring acceleration, always drift off course. </span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<br /></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;">So how about swimming cells? Many swimming cells and microorganisms have the ability to swim in a straight line. Most have no ability to look at a reference point, they can only perceive the liquid they are in immediate contact with. They are also typically top small to be affected by gravity, so have no way of using up or down for reference. They are essentially blind.</span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;"><br /></span></span><span style="background-color: white;"><span style="color: #222222;">The trick for straight line swimming in cells seems to be some kind of spin stabilisation. Way back in 1901, H.S. Jennings noted that many microorganisms spin as they swim, and thought this could be a spin stabilisation somewhat like a spinning bullet. The problem is it can't be. Rugby balls, bullets and spacecraft use spin stabilisation which depends on rotational inertia to keep them spinning and stable, similar to a spinning top. If you made a top that was the size of a cell, and span it in water, it would stop spinning immediately; there is too much friction. <a href="http://www.jstor.org/stable/2453750"><i>The American Naturalist</i>, 35(413):369-379</a></span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;"><br /></span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRPbpen6WOAR4IqVyyelYTZVx49-xoocGgZBJIcnXrbgIMDXOEvXn6XtWAjmR2ciyl8QyKSqnmRe09LimAe0IimSRxx4JaoXsGEEDXH9id6UNblcmWwyhsJJd3wWsv9aM3ORfwrT2WGVk/s1600/Jennings.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="142" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRPbpen6WOAR4IqVyyelYTZVx49-xoocGgZBJIcnXrbgIMDXOEvXn6XtWAjmR2ciyl8QyKSqnmRe09LimAe0IimSRxx4JaoXsGEEDXH9id6UNblcmWwyhsJJd3wWsv9aM3ORfwrT2WGVk/s640/Jennings.png" width="640" /></a></div>
<br /></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;">It turns out the mechanism is just geometry. A person walking is a back-forward/left-right, a 2D, situation. If you curve the walking path it makes it into a looping circle. For a cell swimming there is another direction to think about; in 3D there are two ways to curve the swimming path. The first which curls the path into a circle, and a second which twists the circle to elongate it into a helix-shaped path. Elongate the helix far enough and it turns into a straight line, with the cell rotating as it swims.</span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;"><br /></span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxxteFbkHEr82rMYKcsnkCC-JQK3lyWVRXFb_3HK5hblpz0z-oZDB1zDoevIWyRjVo9pHQQpkdp5mp_Xjm5S_vmSuxCvCsaAuiSHqYWGSFU1shg431ciEEnjqKbboz-MY2gepe-SxWrMg/s1600/Wheeler.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="190" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxxteFbkHEr82rMYKcsnkCC-JQK3lyWVRXFb_3HK5hblpz0z-oZDB1zDoevIWyRjVo9pHQQpkdp5mp_Xjm5S_vmSuxCvCsaAuiSHqYWGSFU1shg431ciEEnjqKbboz-MY2gepe-SxWrMg/s200/Wheeler.png" width="200" /></a></div>
<br />
<span style="background-color: white;"><span style="color: #222222;">The interesting property of the helical swimming paths is their stability. If a cell deliberately twists its swimming path into a helix then small asymmetries (the cellular equivalent of having one leg stronger than the other) won't bend the swimming path into a circle. Instead it just slightly alters the shape of the helix. It can ensure the cell swims in a dead straight line.</span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<br /></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;">My latest paper is all about how cells manage straight line swimming, looking at trypanosome and <i>Leishmania </i>human parasites. Each aspect of swimming has been looked at before, but I believe has never previously been put together as a full story: from mutants with altered cell shape (to add more or less twist), measuring the effect on swimming, and matching this to simulation of how cells achieve their straight line swimming. <a href="http://dx.doi.org/10.1371/journal.pcbi.1005353"><i>PLOS Computational Biology</i>, DOI: 10.1371/journal.pcbi.1005353</a></span></span></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<br /></div>
<div style="font-family: gotham, helvetica, arial, sans-serif; font-size: 14px;">
<span style="background-color: white;"><span style="color: #222222;">There are still big unanswered questions though: Why do parasites need to swim in a straight line? And what are they swimming towards? This is an area of active research, with several major trypanosome research groups (especially <a href="http://www.mimg.ucla.edu/faculty/hill/">Kent Hill</a> and <a href="http://www.zeb.biozentrum.uni-wuerzburg.de/en/people/markus_engstler/">Markus Engstler</a>) interested in addressing these questions.</span></span></div>
Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-6366211132981478852017-01-28T16:35:00.000+00:002017-01-28T17:23:20.674+00:00Molecular Cell Biology of Protozoan Parasites - Ghana 2017Things change fast in Ghana! Three years ago, I helped <a href="http://calculatedimages.blogspot.com/2013/07/cell-biology-of-infectious-pathogens.html">teach a course for young African scientists</a> in the <a href="http://www.ug.edu.gh/">University of Ghana</a> in Accra. This January I got the chance to do the same again, and it has been fantastic. The University of Ghana is becoming a centre of great science in West Africa, with huge contributions by <a href="http://www.ug.edu.gh/bcmb/staff/gordon-awandare-bsc-mphil-ghana-phd-pittsburgh">Gordon Awandare</a> and his West African Centre for Cell Biology of Infectious Pathogens (<a href="http://www.waccbip.org/">WACCBIP</a>) course, funded by the World Bank.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiA2umbshYEk35d5Kn4FQ4kXfFyN6gtTuYRNn9u_yp0k7Krlg0_FO2OAUYeA54YrsynTFdq8JofkNGyVPD_FQQojbYLnaG0GPzltiakq2_k3SgYdeuaAh0MtejN6-vAyUjV_t69svzYm0E/s1600/IMG_20170119_110835_compo.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiA2umbshYEk35d5Kn4FQ4kXfFyN6gtTuYRNn9u_yp0k7Krlg0_FO2OAUYeA54YrsynTFdq8JofkNGyVPD_FQQojbYLnaG0GPzltiakq2_k3SgYdeuaAh0MtejN6-vAyUjV_t69svzYm0E/s640/IMG_20170119_110835_compo.jpg" width="640" /></a></div>
<br />
This time around, our teaching course was made possible by our <a href="http://calculatedimages.blogspot.com/2016/09/tryptagorg.html">TrypTag</a> project, funded by the <a href="https://wellcome.ac.uk/">Wellcome Trust</a>. We applied for extra funds so we could transfer the <a href="http://richardwheeler.net/images/Publications/25567099.pdf">genetic engineering technologies we developed for TrypTag</a> into the hands of African researchers; to get the research techniques to the parts of the world that really suffer from parasitic diseases.<br />
<br />
Our course focused on tools for analysing parasites and what makes them tick, particularly using genetic tools. We mostly looked at <i>Plasmodium </i>(<a href="https://en.wikipedia.org/wiki/Malaria">malaria</a>), <i>Trypanosoma</i> (<a href="https://en.wikipedia.org/wiki/African_trypanosomiasis">sleeping sickness</a>) and <i>Leishmania </i>(<a href="https://en.wikipedia.org/wiki/Leishmaniasis">leishmaniasis</a>). To teach the malaria side of the course we had the excellent <a href="http://vivo.med.cornell.edu/display/cwid-kwd2001">Kirk Deitsch</a> (Cornell University, New York) and <a href="http://www.sanger.ac.uk/people/directory/billker-oliver">Oliver Billker</a> (Sanger Institute, Cambridge). On the trypanosome and <i>Leishmania </i>side we had <a href="http://www.path.ox.ac.uk/content/keith-gull">Keith Gull</a> (University of Oxford) and <a href="http://bms.brookes.ac.uk/staff/dr-sue-vaughan">Sue Vaughan</a> (Oxford Brookes University), along with the TrypTag team: Jack Sunter, <a href="http://richardwheeler.net/contentpages/index.php">Sam Dean</a> and <a href="http://www.sdeanresearch.com/">me</a>!<br />
<br />
So what was the course all about?<br />
<br />
We focused on the tools to help young African scientists (starting their Master's or PhDs) take control of their research - from learning about free genome data and bioinformatics experiments, to computational and genetic tools to make discoveries about parasite biology.<br />
<br />
A major part of the course was tools for handling DNA: PCR for detecting genes in a sample, amplifying DNA to clone it into a plasmid, and working with software (<a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/">ApE</a>) to design cloning strategies for gene tagging, deletion and RNA interference/siRNA knockdown. Teaching how to <i>design</i> a PCR or cloning experiment, rather than just teaching how to do the experimental technique, was very popular.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1Vj_p_id0bMV0Z_HcUN5ywV9tjNZ-25YXYb-OnA1C9f34QfXXgzkoCFeuiVomC_r-j1Oz9ig_4-71SmrMKb-9cE8w_I2NECUD3NWaY9y4gRDSWh2l2lhsm68Z4kHbK64tC-3gOHX3VoM/s1600/IMG_20170121_145446.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1Vj_p_id0bMV0Z_HcUN5ywV9tjNZ-25YXYb-OnA1C9f34QfXXgzkoCFeuiVomC_r-j1Oz9ig_4-71SmrMKb-9cE8w_I2NECUD3NWaY9y4gRDSWh2l2lhsm68Z4kHbK64tC-3gOHX3VoM/s400/IMG_20170121_145446.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNk_KbcfJVPDQCxibQvFFtrC0CY0yiNlfUQocv9T_6S5K8Rl579hLjFuHaGlXGyVXMoNcEMSi29S46ZW9m6fF352H1FZk63UrD5Zx7sIXviY61HupL2XsGtgLRyAVzaEFczOWCNoVK_M0/s1600/IMG_3499.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNk_KbcfJVPDQCxibQvFFtrC0CY0yiNlfUQocv9T_6S5K8Rl579hLjFuHaGlXGyVXMoNcEMSi29S46ZW9m6fF352H1FZk63UrD5Zx7sIXviY61HupL2XsGtgLRyAVzaEFczOWCNoVK_M0/s400/IMG_3499.JPG" width="400" /></a></div>
<br />
We also taught how to use the sequence resources you need for working with DNA: How to get the most from genome databases, like <a href="http://plasmodb.org/">PlasmoDB</a> for malaria and <a href="http://tritrypdb.org/">TriTrypDB</a> for trypanosomes and <i>Leishmania</i>. The course also covered <a href="https://en.wikipedia.org/wiki/Bioinformatics">bioinformatics</a> experiments, thinking how to test a biological hypothesis using existing data from genome data. The students quickly recognised the power of this approach, particularly given genome sequence resources are free! Many were immediately applying these ideas to their areas of research.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3pqdvZ5hG8tOM2oECm2EOj6UVjvZNTxm7pCJkczj55dF5PmebYnEiwAvt6rgt1rnh-eHq1x7Yw-xRDzrLMHVcYk47vzxDsAOPPxvR_hAmtAZlJoPs9Jyw-1AB7Fg2-BwheFZsoH-wb8g/s1600/IMG_20170121_135744.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3pqdvZ5hG8tOM2oECm2EOj6UVjvZNTxm7pCJkczj55dF5PmebYnEiwAvt6rgt1rnh-eHq1x7Yw-xRDzrLMHVcYk47vzxDsAOPPxvR_hAmtAZlJoPs9Jyw-1AB7Fg2-BwheFZsoH-wb8g/s400/IMG_20170121_135744.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgC2u5yuO5nKRLMcJ39j5ZdDg1sLKRZm55XowGB6Pfx2BqevMo9tEXblloL3AR4cg_9aM4gXwMB-bheRceUWJdnErkaraxmY2cEU_NzysuU9zAnDf1ez2hq8PJdJPvF2AEdxN7EkeP-lgQ/s1600/IMG_3545.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgC2u5yuO5nKRLMcJ39j5ZdDg1sLKRZm55XowGB6Pfx2BqevMo9tEXblloL3AR4cg_9aM4gXwMB-bheRceUWJdnErkaraxmY2cEU_NzysuU9zAnDf1ez2hq8PJdJPvF2AEdxN7EkeP-lgQ/s400/IMG_3545.JPG" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
We made sure there was a big push towards critical thinking. The student's loved critical reading of articles in the journal clubs, and thinking about how to apply this critical assessment to their own experiments to make them as good as possible.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipCND5X5FxqYrm-SCUdmcI9vs5sMH9lkpnpUvHeEYQfCwcAVIBSv46HFhtIqNBunY5Uus3B_sitk1bFCAtHBiZ5JqRX3Z932HZFoyk980N9-IH0gIhplDKTuIMCOqqCVbw06PUb7vthvo/s1600/IMG_3574.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipCND5X5FxqYrm-SCUdmcI9vs5sMH9lkpnpUvHeEYQfCwcAVIBSv46HFhtIqNBunY5Uus3B_sitk1bFCAtHBiZ5JqRX3Z932HZFoyk980N9-IH0gIhplDKTuIMCOqqCVbw06PUb7vthvo/s400/IMG_3574.JPG" width="400" /></a></div>
<br />
We also tried, for the first time ever, using the <a href="http://tryptag.org/">TrypTag.org</a> website as the start point for a bioinformatics experiment. The students were challenged to start with a protein localisation patterns to identify protiens likely involved in particular aspects of parasite energy metabolism, then test whether any of these were unique to trypanosomes making them a potential drug target.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5CmNCgvL9BIU0tfINdzt2skFnJ0vlqjqJMJMcc-HOLHdgfdTrYDG53Spdxterc0kW5Dqu1YxSomGRvS2dZZZZ5ujDKVCj-2QAnTAtY6b-JrQphQcm4bTCsLZcxwK6bKWWbpUbbmz2-OE/s1600/IMG_20170124_145857.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5CmNCgvL9BIU0tfINdzt2skFnJ0vlqjqJMJMcc-HOLHdgfdTrYDG53Spdxterc0kW5Dqu1YxSomGRvS2dZZZZ5ujDKVCj-2QAnTAtY6b-JrQphQcm4bTCsLZcxwK6bKWWbpUbbmz2-OE/s400/IMG_20170124_145857.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3gg6G42QLy-uw0OH_faOyNExAE96F5SZZbl3bAJ6fnNKhtdG9dViHNvL9lrXdlhhx9Pb0iu7BSh6XEZnNipwBaVBrp1wa1crj0Y2PE-XUA9AiHC-Pe0wXpXyF9486XT-87SUhMfn4eG0/s1600/FullSizeRender+8.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3gg6G42QLy-uw0OH_faOyNExAE96F5SZZbl3bAJ6fnNKhtdG9dViHNvL9lrXdlhhx9Pb0iu7BSh6XEZnNipwBaVBrp1wa1crj0Y2PE-XUA9AiHC-Pe0wXpXyF9486XT-87SUhMfn4eG0/s400/FullSizeRender+8.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
This was the perfect stress test for the new <a href="http://tryptag.org/">TrypTag.org</a> website and server. It coped with up to a page view per second, and downloads of 10 images per second, with no problems. All over a slightly unreliable internet connection in Ghana! Many thanks to the scientific computing at the <a href="http://www.path.ox.ac.uk/">Sir William Dunn School of Pathology</a> in Oxford for helping make this happen.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_NUQsW6Iw8Sy3XadxppmkC4UV8CXRlNkloFaEclEMIyThpL3L2lVbIgmLZtTShxd29sowELiRXh24aSCKtqsr8IgEXE7DGijE7c2HZY9CAp_FshoH05hQnVJ0y9k1V_8sb1omc6jycGE/s1600/newusers_pageviews.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="253" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_NUQsW6Iw8Sy3XadxppmkC4UV8CXRlNkloFaEclEMIyThpL3L2lVbIgmLZtTShxd29sowELiRXh24aSCKtqsr8IgEXE7DGijE7c2HZY9CAp_FshoH05hQnVJ0y9k1V_8sb1omc6jycGE/s400/newusers_pageviews.png" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: left;">
Overall the course was a great success, with very positive feedback from the students and local research staff. The students were smart, engaged and hard-working. It will be exciting to see what these young people can achieve over the next few years.</div>
Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-74178917680018020682016-09-05T13:24:00.005+01:002016-09-06T08:06:20.166+01:00TrypTag.org<link href="https://fonts.googleapis.com/css?family=Roboto:100,300,400,500,400italic,500italic" rel="stylesheet" type="text/css"></link>
The website for one of my new major research projects <a href="http://tryptag.org/">is now live!</a><br />
<br />
<h1 style="font-family: roboto, sans-serif; font-size: 70px; font-weight: 100; text-align: center;">
<a href="http://tryptag.org/" style="color: rgba(56 , 142 , 60 , 1.00); font-family: "roboto" , sans-serif; font-size: 70px; font-weight: 100; text-align: center;" title="TrypTag.org">
TrypTag<span style="font-size: 50%; font-weight: 300;">.org</span></a></h1>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUIhy0wS-_xjKPPXlgpkN9A23E0MCskCY6cqMURn_BX7ml_P_ipN_2xFgrc6huzZjRXDLUTWNlSSdQd4AIAQibhg-xe_yBOtDIdd567YgfogzoApAdraX6SyZ_v-ER9Ii0UKwvHBhRtaU/s1600/TrypTagBlog.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="194" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUIhy0wS-_xjKPPXlgpkN9A23E0MCskCY6cqMURn_BX7ml_P_ipN_2xFgrc6huzZjRXDLUTWNlSSdQd4AIAQibhg-xe_yBOtDIdd567YgfogzoApAdraX6SyZ_v-ER9Ii0UKwvHBhRtaU/s640/TrypTagBlog.jpg" width="640" /></a><br />
<br />
<a href="http://tryptag.org/">TrypTag </a>is a project to tag every gene in the trypanosome genome with a fluorescent marker to see where it goes in the cell.<br />
<br />
Do you have no idea what I'm talking about? Read on to see what all that jargon means!<br />
<br />
<b>Trypanosomes </b>are one of the parasites my research involves. They are single cell parasites that live in the blood, and they cause the diseases sleeping sickness in humans and nagana in livestock across Africa. All in all, not very nice.<br />
<br />
Like all cells, trypanosomes are made up of protein machinery. Each protein is encoded by a <b>gene </b>in genome. A first step in finding a protein's function is finding where it goes in the cell. If you can map it to a particular structure then you have a good idea it's going to function there too.<br />
<br />
To find where a protein goes in a cell we genetically modify the cell, sticking a fluorescent marker to the protein so we can see where it goes using a microscope. This is the process of <b>tagging</b>.<br />
<br />
We are going to tag every protein gene in the genome, around <b>8000 genes</b>, and build a complete map of the protein composition of the cell.<br />
<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-52529199822932939802016-02-16T15:51:00.004+00:002016-02-16T15:58:51.909+00:00Looking at the structure inside cells<div class="separator" style="clear: both;">
How complex and structured is the inside of a cell? It's hard to imagine, but the internal organisation of cells is typically precisely controlled by molecular skeletons and scaffolds, giving cells the shape they need to function.</div>
<div class="separator" style="clear: both;">
<br /></div>
<div class="separator" style="clear: both;">
We can discover the 3D organisation of the inside of cells using <a href="https://en.wikipedia.org/wiki/Electron_tomography">electron tomography</a>; a process where you capture a series of images with an electron microscope, with the sample tilted at a slightly different angle for each image. This can then be used to calculate the 3D shape of the sample, using the same maths as for an <a href="https://en.wikipedia.org/wiki/CT_scan">X-ray CT scan</a>.</div>
<div class="separator" style="clear: both;">
<br /></div>
<div class="separator" style="clear: both;">
<i><a href="https://en.wikipedia.org/wiki/Leishmania">Leishmania</a></i> parasites are exquisitely structured. While they are only 2 micrometres wide (100 would fit across a human hair) they have a precise internal organisation which they faithfully replicate each time they divide. One of the distinctive parts of this organisation is the flagellar pocket, where the cell membrane folds in on itself at the base of the whip-like <a href="https://en.wikipedia.org/wiki/Flagellum">flagellum</a> that the cell uses to swim.</div>
<div class="separator" style="clear: both;">
<br /></div>
<div class="separator" style="clear: both;">
In my latest paper, "<a href="http://jcs.biologists.org/content/129/4/854">Flagellar pocket restructuring through the <i>Leishmania</i> life cycle involves a discrete flagellum attachment zone</a>", I used electron tomography to reconstruct the three-dimensional organisation of the Leishmania flagellar pocket. The structure in this area of the cell is incredible, and the journal picked a rendering of it for the cover image.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwoUBl17AdTLsxP1ingJssibPbPwr1pAsZfDqbxWx0WltFsR2_wN0WD1RM0ingxj4EX1WjG-ynTFdL5DUVcqW0wEfKZO39UvbHr_2teusbHxq2r7PJCJsVFPRZrO03zztp2uNOYQwwMnc/s1600/Cover.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwoUBl17AdTLsxP1ingJssibPbPwr1pAsZfDqbxWx0WltFsR2_wN0WD1RM0ingxj4EX1WjG-ynTFdL5DUVcqW0wEfKZO39UvbHr_2teusbHxq2r7PJCJsVFPRZrO03zztp2uNOYQwwMnc/s640/Cover.png" width="488" /></a></div>
<br />
Volume covered in this 3D reconstruction is only 3 by 2 by 1 micrometres, about the size of a typical bacterial cell, but has enormous complexity. I have shown the <a href="https://en.wikipedia.org/wiki/Microtubule">microtubules</a> (which make up most of the cytoskeleton) in red and membranes in blue. Each microtubule is only about 5 molecules wide, and is about 10,000 times narrower than a human hair! Some other specialised parts of the cytoskeleton are in green.<br />
<br />
You can download the paper for free <a href="http://jcs.biologists.org/content/129/4/854.long">here</a> to take a look at the structures in this area of the cell in more detail.<br />
<br />
Software used:<br />
<a href="http://bio3d.colorado.edu/imod/">IMod</a>: Electron tomography structure<br />
<a href="https://www.blender.org/">Blender</a>: Tidying and rendering of the 3D structureUnknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-73083468977972848252015-11-08T13:24:00.000+00:002016-02-16T15:58:41.184+00:00Ergodic Analysis<a href="http://www.richardwheeler.net/images/Publications/26543196.pdf">My review paper about ergodic analysis</a> came out on Thursday. Does ergodic analysis sound terrifying? It's actually quite a simple concept and it is a powerful method for extracting information about the dynamics of a cell division cycle from a single snapshot of cells at random stages of the cell cycle.<br />
<br />
Ergodic analysis is particularly useful if a time-lapse video is impossible, for example if the cells swim or you want to do an analysis that kills the cells.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.richardwheeler.net/hosting/calculatedimages/RichardWheeler_ErgodicAnalysis.pdf"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPc7SXqRccjG8HAeANcknbDEavimotfYoACidUG2vvJNcXTftBvc0cOZ504NH0ARHzsifG4ttXCAUcNtY1MGyUro4dLlsyKBVK01ytZhGq1EecmT-KJFh2UZyy60fz7xansdSLV_hGTbw/s640/Ergodic.png" width="452" /></a></div>
<br />
Does this sound interesting for your research? Drop me a message: <a href="https://twitter.com/Zephyris">@Zephyris</a>.<span id="goog_1842147773"></span><span id="goog_1842147774"></span><a href="https://www.blogger.com/"></a><br />
<br />
Software used:<br />
<a href="http://www.autodesk.com/products/sketchbook-pro/overview">Autodesk Sketchbook Pro</a>: Drawing the cells.<br />
<a href="http://inkscape.org/">Inkscape</a>: Page layout.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-46060846563310270952015-06-01T22:39:00.001+01:002015-06-03T21:40:55.879+01:00Pebbling in colourThe <a href="https://getpebble.com/pebble_time">Pebble Time</a> is finally out! This fantastically simple, yet massively functional, little smartwatch is now shipping to the <a href="https://www.kickstarter.com/projects/597507018/pebble-time-awesome-smartwatch-no-compromises">Kickstarter</a> backers who pledged their renewed support to the company that produced the original <a href="http://calculatedimages.blogspot.de/2013/05/pebble.html">Pebble</a>.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeLPYcNUWPBzZfCB0B77rSB1HS-HFzqJZZ4F_cyIk3Pjv60rGiZ6I4tVakZ1eKH_lQZWkjfxIa37o5zDVSspg8gGAPuaTHqGP9CAa3OnZ70vsHJr_YueZmdU5-RmaDF7KLxBC-Jkhgr5Y/s1600/AniV1_stabilised_720Crop_loop_mindif.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="284" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeLPYcNUWPBzZfCB0B77rSB1HS-HFzqJZZ4F_cyIk3Pjv60rGiZ6I4tVakZ1eKH_lQZWkjfxIa37o5zDVSspg8gGAPuaTHqGP9CAa3OnZ70vsHJr_YueZmdU5-RmaDF7KLxBC-Jkhgr5Y/s640/AniV1_stabilised_720Crop_loop_mindif.gif" width="640" /></a><br />
<br />
I've been lucky enough to be beta testing a developer preview model of the Pebble Time, and have had it on my wrist for the last few weeks. I used this time to put together some animated watchfaces which make the most of the colour screen, and learn some C programming along the way!<br />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<hr />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div style="text-align: center;">
<a href="https://apps.getpebble.com/en_US/application/5504b3815a96dcf0c6000023"><span style="font-size: large;">Path Time</span></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://apps.getpebble.com/en_US/application/5504b3815a96dcf0c6000023"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigQC2Sp3hVhqKJNS6grDmNhh3wsO6GJZ-u1krf22RFKDZR5OC_K2Y4TCoV1MRRXTH9M2ddHV8lod6fD19smAvxryqwxJNXhRhewwUJadEAicR8MFuoRW70Pouw8VaJK0ptU4p_I9jRb9o/s1600/Animation.gif" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: left;">
An elegant animated watchface, with each digit built from curving paths. Animated minute transitions, and tap-triggered animation to improve readability under low light. Animations, line widths and colours can be customised.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Inspired by the watchface shown on the red Pebble Time Steel advertising images:</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjd_Ssd6fvAO-dGGVzYF6uzwtT5YOCHqjgScufRCkSsvC_VZnKDTd_WVItcwrTxWjLIwiV64Kf0ZeZaLop5F_JEY6BCxJ88GOrQJq4_2eGR2DTl1UzR7U5ADjb0WQv8TOepr32fDNMXSy8/s1600/128c19f22095b6067de563f107d639a5_original.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjd_Ssd6fvAO-dGGVzYF6uzwtT5YOCHqjgScufRCkSsvC_VZnKDTd_WVItcwrTxWjLIwiV64Kf0ZeZaLop5F_JEY6BCxJ88GOrQJq4_2eGR2DTl1UzR7U5ADjb0WQv8TOepr32fDNMXSy8/s320/128c19f22095b6067de563f107d639a5_original.png" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<hr />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: large;"><a href="https://apps.getpebble.com/en_US/application/556cc05546b00ed71100003c">Pop!</a></span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://apps.getpebble.com/en_US/application/556cc05546b00ed71100003c"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIlaEQ_TVEZ91i3dVXwaLssyTrS5EbFhMFYLLTZoaxwdY2p5IWDilMDLXXR6_tOP7RUEtB_CxTOLBl-WvERv2QGft6BzGjHVMFJxl_XGnR3g3QfvQtFn-t8ltWCyU9wiGe7yQYr-asU4k/s1600/18.27.Mon.1.Jun_Ani_Opt.gif" /></a></div>
<br />
<div style="text-align: center;">
<br /></div>
A fun, animated, easy to read watchface. Every minute the bubbles in the background pop, and a set of new ones appear (by default) in a new colour. Alternatively you can customsise the colour of the bubbles. Tapping or shaking the watch also triggers the animation.<br />
<br />
Inspired by the watchface shown on the red Pebble Time advertising images:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7llcSzFLm1gJEzZ6XfLGLKB46BlCgclNuzvdWVzqGlx3dEWE7qaJ9ynvjzPRQMQBoiNrTrK35rY4RhAwfUXtcTG7lSywZxRRquzh36knuiUI420EXpXEBVJ482SwcRKjeGhx4PPFvS18/s1600/61157aa33fccb728016e87f97d870330_original.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7llcSzFLm1gJEzZ6XfLGLKB46BlCgclNuzvdWVzqGlx3dEWE7qaJ9ynvjzPRQMQBoiNrTrK35rY4RhAwfUXtcTG7lSywZxRRquzh36knuiUI420EXpXEBVJ482SwcRKjeGhx4PPFvS18/s320/61157aa33fccb728016e87f97d870330_original.png" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<hr />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div style="text-align: center;">
<span style="font-size: large;"><a href="https://apps.getpebble.com/applications/5561e3acfd8f4b0a2c000079">Arcturus</a></span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://apps.getpebble.com/applications/5561e3acfd8f4b0a2c000079"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRQK0vn9sr2_msrtZ6MUjFan2Vw6Ucoyy3NmHQXECBPSscFGJbaa2yaD_-D_poWXhiyPW0i7dwhLezeTV2j07KHiegk8fg0QiMr2DiV_z3hTMnqCkA1uY1qMo4d_n8ltBmRHW0X1PjAq0/s1600/7.20.47_DoubleAni_Auto.gif" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
A colourful interpretation of the classic arc watchface design, with a Pebble Time-style loading animation and dynamic colour schemes. Colour schemes and whether or not to show the second hand can be customised.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<hr />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div style="text-align: center;">
<a href="https://apps.getpebble.com/en_US/application/5564ce8fda25f6977c00007b"><span style="font-size: large;">Disarray</span></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://apps.getpebble.com/en_US/application/5564ce8fda25f6977c00007b"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4j_xocxJ9kQVHZ0UuI4NiF9wV-zUa_bmOEKTXm8dkpOdYcW7XujL_WTxxVgixnWiT1I662MUBQA8k3WECwiGahyLWRWyXMgSiJhwFvzoFubHmFfsghOeByCIyDt_MLoX9amwg-bSzyLs/s1600/SweepFlip_Ani_Proc%2527d.gif" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
A colourful interpretation of the classic pixel array digital watchface design, with loading animations, animated minute transitions and dynamic colour schemes. Colour schemes, pixel styles and animations can be customised.</div>
<div style="text-align: left;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<hr />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<b>Software used:</b><br />
<a href="https://cloudpebble.net/ide/">CloudPebble</a>: Watchface programming. CloudPebble is an online IDE for Pebble watchfaces and apps.<br />
<a href="https://notepad-plus-plus.org/">Notepad++</a>: Server side HTML/Javascript for the watchface settings.Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-1382329114149565542.post-53062347694699318602015-04-17T14:04:00.000+01:002015-04-17T14:05:53.676+01:00Light-Years of DNALight-year, and DNA. Not two scientific terms you expect to see on the same page, but over your lifetime your body will produce around one light-year of DNA! That is about one trillion kilometres. Don't believe me? Let's do some maths:<br />
<br />
Every cell in your body has two copies of your genome, held in 23 pairs of chromosomes. The human genome is approximately three billion (3×10<sup>9</sup>) base pairs of DNA.<br />
<br />
The famous double helix of DNA has about 10 base pairs per twist, and each twist is 3.4 nanometers long (3.4×10<sup>-9</sup> metres, the same as roughly 20 carbon-carbon bonds).<br />
<br />
This means that the total length of DNA contained in every cell of your body is approximately 2 meters (3×10<sup>9</sup> base pairs multiplied by 0.34×10<sup>-9</sup> metres per base pair, doubled because of the two copies).<br />
<br />
Your body has about ten trillion (1×10<sup>13</sup>) cells (excluding red blood cells), and this remains roughly constant through your life. There is a huge turnover of these cells though, as your body replaces cells to maintain itself.<br />
<br />
Every time a cell is replaced its 2 metres of DNA must be produced. In most tissues the cells are replaced in a couple of months, and in many they are replaced in just a couple of days. Even cells in bones are replaced every few years.<br />
<br />
The average lifetime of a cell is probably one or two months, so if you live to 80 then your cells are replaced about 500 times throughout the course of your life.<br />
<br />
This means that the total length of DNA your body produces in your lifetime is approximately 1×10<sup>16</sup> metres (2 metres multiplied by 1×10<sup>13</sup> cells, multiplied by 500 replacements). 1×10<sup>16</sup> metres (ten thousand trillion metres) is about one light-year (0.946×10<sup>16</sup> metres)! Most amazingly it would not be a light-year of random DNA sequence, but ten thousand trillion identical copies of your DNA, faithfully replicated by your cells.<br />
<br />
References:<br />
<a href="http://informahealthcare.com/doi/abs/10.3109/03014460.2013.807878">An estimation of the number of cells in the human body</a><br />
<a href="http://book.bionumbers.org/how-quickly-do-different-cells-in-the-body-replace-themselves/">How quickly do different cells in the body replace themselves?</a><br />
Thanks to Rob Phillips for making me think about this!Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-1382329114149565542.post-8021378852737903472015-03-22T22:17:00.004+00:002015-03-22T22:18:19.523+00:00Partial Solar Eclipse 2015<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijjdLWNKvxLTMNU47GeivaoZMdqc-awDo3Xw0kLEfrVPAnQOyMlMBiNBiHxLfureCNgqBN4I-c90AeApqFgRkuHtHI2ReHyD_2bKXHxxl-2HJ6Q59tMPzRJ6zgwiNHZZKz7aBOsP07LRs/s1600/composite.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijjdLWNKvxLTMNU47GeivaoZMdqc-awDo3Xw0kLEfrVPAnQOyMlMBiNBiHxLfureCNgqBN4I-c90AeApqFgRkuHtHI2ReHyD_2bKXHxxl-2HJ6Q59tMPzRJ6zgwiNHZZKz7aBOsP07LRs/s1600/composite.jpg" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
[Obligatory partial <a href="http://en.wikipedia.org/wiki/Solar_eclipse_of_March_20,_2015">solar eclipse</a> post, as seen from Dresden, Germany]</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-79862794420121269092015-01-28T16:56:00.001+00:002015-02-06T10:54:29.423+00:00Smooth Videos - AKA Correcting NASAWhat makes a video look smooth? Your eye is extremely sensitive to problems with videos, and for any video to look smooth it has to have:<br />
<br />
<ul>
<li>A high frame rate</li>
<li>A steady camera</li>
<li>Roughly even brightness each frame</li>
</ul>
<br />
Normally these are easy to get. Any modern camera will give a decent frame rate, and the exposure time for each shot will be accurate, giving an even brightness of images each frame. Camera steadiness is more difficult, but a basic tripod will solve that.<br />
<br />
This is a lot harder in space! For a NASA space probe floating through deep space, keeping a steady orientation is a challenge. Spacecraft can do this well quite well, using thrusters and reaction wheels. They still make some small mistakes though. Getting an even exposure time for each frame of a video is also harder in deep space, especially as it might take minutes or hours for radio commands to reach the space probe so you have to trust its autoexposure. Luckily, given ok starting material, correcting camera shake and frame brightness problems by image processing is quite easy.<br />
<br />
NASA's Dawn space probe is currently approaching Ceres, getting sharper pictures of this dwarf planet than ever before. A series of these pictures even shows this tiny world rotating. Unfortunately, they didn't correct the shake or brightness problems in the video released to the press:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh43kcbKifW0LQr8hQiqaPIu6Y3G2vPIRU2dhJQkpDrcq8IBp2fIZOMH-diZXHf-Sr4qFFy4d0rRVn0mY1jyVglXSvCamUdMrRt4_k_7_c8VyrKwC_QADRZ-zs2vbmhEO-MntT21-rYiRE/s1600/opnav1.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh43kcbKifW0LQr8hQiqaPIu6Y3G2vPIRU2dhJQkpDrcq8IBp2fIZOMH-diZXHf-Sr4qFFy4d0rRVn0mY1jyVglXSvCamUdMrRt4_k_7_c8VyrKwC_QADRZ-zs2vbmhEO-MntT21-rYiRE/s1600/opnav1.gif" height="400" width="399" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://dawn.jpl.nasa.gov/multimedia/Animation_of_Ceres.asp">NASA/JPL-Caltech/UCLA/MPS/DLR/IDA/PSI</a></div>
<br />
A quick fix in ImageJ to remove the shake and even out the frame brightness makes a (dwarf) world of difference:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhED6SMVVZCPdx-mK6UKj94RgEt5P8CVrP-DIf0q9jO3q3NpxNZ2IgEd0NkgCFqIb-Bm1i9m_6uvjz9ui3upWaUMl0OBTj4qOlfIgVseAFYpkRnAnK057W48Abv3v_Ft106gRiveJR75Vo/s1600/Ceres.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhED6SMVVZCPdx-mK6UKj94RgEt5P8CVrP-DIf0q9jO3q3NpxNZ2IgEd0NkgCFqIb-Bm1i9m_6uvjz9ui3upWaUMl0OBTj4qOlfIgVseAFYpkRnAnK057W48Abv3v_Ft106gRiveJR75Vo/s1600/Ceres.gif" height="400" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
Adapted from <a href="http://dawn.jpl.nasa.gov/multimedia/Animation_of_Ceres.asp">NASA/JPL-Caltech/UCLA/MPS/DLR/IDA/PSI</a></div>
<br />
As the probe gets closer and closer to Ceres its shots are getting more and more spectacular, but the videos still need shake and brightness correction.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlmAcG4N6yVgMl6n3vetreDaqiLVIxQMKINxMhMktLB8fGJxId74nQP7c54650h2_L-UO0V_M-Ax61gTEV2liDw3mwN3zUST1GVLq6XS6OG3J-mACBd5jQt_JDgTsxxSx4dzhy3dvRDJ0/s1600/Ceres2.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlmAcG4N6yVgMl6n3vetreDaqiLVIxQMKINxMhMktLB8fGJxId74nQP7c54650h2_L-UO0V_M-Ax61gTEV2liDw3mwN3zUST1GVLq6XS6OG3J-mACBd5jQt_JDgTsxxSx4dzhy3dvRDJ0/s1600/Ceres2.gif" height="400" width="400" /></a></div>
<div style="text-align: center;">
Adapted from <a href="http://dawn.jpl.nasa.gov/multimedia/Sharper_than_ever_animation.asp">NASA/JPL-Caltech/UCLA/MPS/DLR/IDA/PSI</a></div>
<br />
Interested in improving some NASA videos? I did the corrections using the free scientific image editing software <a href="http://imagej.nih.gov/ij/">ImageJ</a>, and these are two handy macro scripts for video corrections in ImageJ:<br />
<br />
Image stabilisation<br />
<pre>
//Stabilise based on signal intensity centroid (centre of gravity)
//Stabilises using translation only, using frame 1 as the reference location
//This method is suitable for stabilising videos of bright objects on a dark background
for (z=0; z<nSlices(); z++) {
//For each slice
setSlice(z+1);
//Do a weighted sum of signal for centroid determination
sxv=0;
syv=0;
s=0;
for (x=0; x<getWidth(); x++) {
for (y=0; y<getHeight(); y++) {
v=getPixel(x, y);
sxv+=v*x;
syv+=v*y;
s+=v;
}
}
//Calculate the centroid location
cx=sxv/s;
cy=syv/s;
if (z==0) {
//If the first slice, record as the reference location
rcx=cx;
rcy=cy;
print(rcx, rcy);
} else {
//Otherwise calculate the image shift and correct
dx=cx-rcx;
dy=cy-rcy;
print(dx, dy);
makeRectangle(0, 0, getWidth(), getHeight());
run("Copy");
makeRectangle(-dx, -dy, getWidth(), getHeight());
run("Paste");
}
}
</pre>
Brightness normalisation<br />
<pre>
//Normalise image brightness to reduce video flicker
//Scales intensity based on the mean and standard deviation, using frame 1 as the reference frame
//This method is suitable for reducing flicker in most videos
for (z=0; z<nSlices(); z++) {
//For each slice
setSlice(z+1);
//Find the signal mean and standard deviation
run("Select All");
getRawStatistics(area, mean, min, max, stdev);
if (z==0) {
//If the first slice, record as the reference signal mean and stdev
rmean=mean;
rstdev=stdev;
print(rmean, rstdev);
} else {
//Otherwise calculate the brightness and scaling correction
run("Macro...", "code=v="+rmean+"+"+rstdev+"*(v-"+mean+")/"+stdev);
print(mean, stdev);
}
}
</pre>
<div>
Software used:</div>
<div>
<a href="http://imagej.nih.gov/ij/">ImageJ</a>: Image corrections</div>
<div>
<a href="http://www.gimp.org/">GIMP</a>: Animated gif file size optimisation</div>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-13103259002503497102015-01-22T09:14:00.001+00:002015-01-22T10:29:12.812+00:00Tengwar - Transliterating Font<i><span style="font-size: x-small;">This blog post is about a Tengwar font I designed. It <b>automatically</b> converts text as you type into accurate Elvish script. You can download it for free <a href="https://www.myfonts.com/fonts/zephyris/tengwar-transliteral/">here</a>. Just make sure you enable ligatures, contextual alternates and kerning for best results!</span></i><br />
<i><span style="font-size: x-small;"><br /></span></i>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<i><span style="font-size: x-small;"><br /></span></i>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFTgb6rtXlZSB86necNVkL8QZqIM09giMJEdkgK5uKjrDDixe6bmrixwO1ryfwgtmDljuYMZZgk4yLxItDrZPA_-qtXsqPXcewZC-1zlpWD-WRnlEBea8GeCXHeMdPLij06zneLdkTTWY/s1600/TengwarStack_Crop_Loop_Annotated_Opt2.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFTgb6rtXlZSB86necNVkL8QZqIM09giMJEdkgK5uKjrDDixe6bmrixwO1ryfwgtmDljuYMZZgk4yLxItDrZPA_-qtXsqPXcewZC-1zlpWD-WRnlEBea8GeCXHeMdPLij06zneLdkTTWY/s1600/TengwarStack_Crop_Loop_Annotated_Opt2.gif" height="315" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmGyp8MZ4C1T2tR4ydX_GzcHSaWR6kbJ_ZOJe-SzikQj4YGBrGCHpawunlWjgtrpIJBjIkmAtzi6zI4yvB9t7qYCTCBir3z8rLmqdwVwhEsg7C2-2u54WcLr8OMReOmPvLOQg8TcvCob8/s1600/Intro.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmGyp8MZ4C1T2tR4ydX_GzcHSaWR6kbJ_ZOJe-SzikQj4YGBrGCHpawunlWjgtrpIJBjIkmAtzi6zI4yvB9t7qYCTCBir3z8rLmqdwVwhEsg7C2-2u54WcLr8OMReOmPvLOQg8TcvCob8/s1600/Intro.png" height="90" width="640" /></a></div>
<br />
While writing his Middle Earth books, JRR Tolkein invented an entire alphabet for the elves called Tengwar. His attention to detail was incredible, Tengwar is a fully functioning writing system. This is the famous Elvish writing seen all through Lord of The Rings and the Hobbit.<br />
<br />
Tengwar is an alphabet, not a language, and can be used to write many languages. This is like, for example, Latin and Greek alphabets; the word English word “ring” is normally written in the Latin alphabet but could also be written in the Greek alphabet as “ρινγ”. The two sound the same, it is just a different way of writing the sounds of the word “ring”. The process of transferring a word between two different alphabets is called transliteration.<br />
<br />
In Middle Earth, Tengwar is one of the major ways of writing. Many languages were written in Tengwar: two Elvish languages called Sindarin and Quenya, the Black Speech of Mordor (on the One Ring), and the language of men (English). Tolkein gave detailed notes on how to write English in the Tengwar alphabet. In Tengwar “ring” is written:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEVSznqxlxmMM_pO5LeBi62TK46EoNPe2kr7Bcp3O6AmHN8u8dZ36CgqRLAVYLK1-Aj9hfPUmsnBq6x84aOf9I8c98t9DhS0Uy0fDgVybh5qGLR8zOZxmD91MDNAKnCcbexWoNi3lLlrQ/s1600/ring1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEVSznqxlxmMM_pO5LeBi62TK46EoNPe2kr7Bcp3O6AmHN8u8dZ36CgqRLAVYLK1-Aj9hfPUmsnBq6x84aOf9I8c98t9DhS0Uy0fDgVybh5qGLR8zOZxmD91MDNAKnCcbexWoNi3lLlrQ/s1600/ring1.png" height="60" width="640" /></a></div>
<br />
Writing in Tengwar follows simple rules but quickly gets complicated, so I designed a font that does it automatically! You can download it for free <a href="https://www.myfonts.com/fonts/zephyris/tengwar-transliteral/">here</a>. As far as I know this font is unique, all other Tengwar fonts are just collections of symbols you have to manually mix and match.<br />
<br />
To use this font you just need to download and install it. Once it is installed, just select it as the font and start typing as normal. The font will <i>automatically </i>transliterate the text you type into accurate Tengwar, based on Tolkein’s rules about writing English in Tengwar.<br />
<br />
To make sure the font is working accurately you need to make sure three settings are enabled: kerning, contextual alternates and ligatures. For example, in Microsoft Word you can do this through the advanced font settings:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiVk_zccZSccXuiAQjdDrdfjyrMesHCgJbFhukHuOVklFhewN3IDHOCotKh_ti8QOQWL0lIN1GZ1CJCD3rSpaEPfrzok4JDjs1A6s5dozDdN-pyq0Y5XfZWXpiRHe6fo2xkcaUVTasWDmc/s1600/Settings1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiVk_zccZSccXuiAQjdDrdfjyrMesHCgJbFhukHuOVklFhewN3IDHOCotKh_ti8QOQWL0lIN1GZ1CJCD3rSpaEPfrzok4JDjs1A6s5dozDdN-pyq0Y5XfZWXpiRHe6fo2xkcaUVTasWDmc/s1600/Settings1.png" height="255" width="320" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgV7lLDNNCCO3inB9-GwnHnKm3ZlnlUfTfYlNjFMjQeemRaMcKx80V1ZR-AxtDQItiz1VHF3WTODibL0IYSs6Zg-VFv1pJ56shEF6NpD8jyl-AQqqwOezyS-jkrJEPjS1eurwj7hG8EkF0/s1600/Settings2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgV7lLDNNCCO3inB9-GwnHnKm3ZlnlUfTfYlNjFMjQeemRaMcKx80V1ZR-AxtDQItiz1VHF3WTODibL0IYSs6Zg-VFv1pJ56shEF6NpD8jyl-AQqqwOezyS-jkrJEPjS1eurwj7hG8EkF0/s1600/Settings2.png" height="320" width="319" /></a></div>
<br />
So how does it work? Basic Tengwar is similar to the Latin alphabet, with two classes of symbols representing the sounds of different consonants and different vowels. At the simplest level, to write the word “ring” the font just selects the four symbols for “r”, “i”, “n” and “g”:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4XYMTA86a0T2eYE8lCfB3eTwTT-vyqmhEbbVcr2_TUgXe-PDDDL2R_M1_yJFZV-UmEWbzl5opkq1VlwuKGZLRflG-MHabREy-CxGelpAfldpX_DZ502Z5Fne-TzpAdU_RLeDykpWZL0Q/s1600/ring2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4XYMTA86a0T2eYE8lCfB3eTwTT-vyqmhEbbVcr2_TUgXe-PDDDL2R_M1_yJFZV-UmEWbzl5opkq1VlwuKGZLRflG-MHabREy-CxGelpAfldpX_DZ502Z5Fne-TzpAdU_RLeDykpWZL0Q/s1600/ring2.png" height="184" width="640" /></a></div>
<br />
Unlike the Latin alphabet, there are special rules for how vowels are written. Instead of always being a separate letter, if a vowel comes immediately before a consonant it is written as an accent on that consonant. In “ring” the “i” comes immediately before the “n” so the font writes it as an accent on the “n”:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb9roDwq23M0WBLzgAYQEQ6wZL1knfNB3hZyBNG4YZnhHZ21Uo6JmDp14DLg1QuDrvURndgF1l0D-2trPkylZJjqHcGq6CO2ZTJReOn4nMpJQ0hd7yuZXjuajlyZ_qbvvnwRVg1AdTdMw/s1600/ring3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb9roDwq23M0WBLzgAYQEQ6wZL1knfNB3hZyBNG4YZnhHZ21Uo6JmDp14DLg1QuDrvURndgF1l0D-2trPkylZJjqHcGq6CO2ZTJReOn4nMpJQ0hd7yuZXjuajlyZ_qbvvnwRVg1AdTdMw/s1600/ring3.png" height="90" width="640" /></a></div>
<br />
There are some special rules to use for some consonants, depending on where they are in a word. “r” is one of these letters. If it is followed by a vowel then it should have a different symbol, which the font automatically selects:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEha5VL36i4PulP5mLlfMKuwJ7wlYNA94zxNi263z0zsNHW-vG67lRulqyPV9nr-ILPMQTVdcaZMEdqTc_lCLee2YskdhX_DK-coFkA5WimoL6qV17-5z589d_YmotOdRnSWb-sXyeC5eqc/s1600/ring4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEha5VL36i4PulP5mLlfMKuwJ7wlYNA94zxNi263z0zsNHW-vG67lRulqyPV9nr-ILPMQTVdcaZMEdqTc_lCLee2YskdhX_DK-coFkA5WimoL6qV17-5z589d_YmotOdRnSWb-sXyeC5eqc/s1600/ring4.png" height="88" width="640" /></a></div>
<br />
Finally, some common combinations of consonants that have a single sound (like “th” as in “the”, “ch” as in “church” and “gh” as in “ghost”) have their own single symbol. “ng” is one of these pairs and, again, the font automatically makes this substitution:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWo3W_rcoqykJrzgdi2p7fZOgFvv6-cykp2kQSlQLNQFCk_GK6a9o8czEt7QJWYUtLhMui8_vb9mZeDMyhaXuvo4uMEsnBHQ9UZFeqzPfe2bBQQyi0wa1bktAyskK84wqTrdzcUPIHohE/s1600/ring5.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWo3W_rcoqykJrzgdi2p7fZOgFvv6-cykp2kQSlQLNQFCk_GK6a9o8czEt7QJWYUtLhMui8_vb9mZeDMyhaXuvo4uMEsnBHQ9UZFeqzPfe2bBQQyi0wa1bktAyskK84wqTrdzcUPIHohE/s1600/ring5.png" height="84" width="640" /></a></div>
<br />
And that is how the font automatically writes “ring” in Tengwar. These are not the only rules though, there are also other ones built into the font that involve double vowels, double consonants, the letter “n” preceding another consonant, whether a “y” is used as a vowel or a consonant, whether an “e” is voiced in a word or is silent at the end of a word, etc.<br />
<br />
The key feature of my font is that it takes all of these rules into account <i>automatically</i> and lets you simply type away as normal and get an accurate, readable result in Tengwar. You can also just select an existing chunk of text and apply the font to it to transliterate it to Tengwar, but make sure the text is all lower case for best effect. It does make a few very small mistakes, but Tolkein would understand it!<br />
<br />
Tengwar is a beautiful and concise alphabet. The way vowels, double letters and letter pairs combine make many words very short and elegant:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgurrMiNLpG8Sg7NYKWLtt1bjQZbRg9UyRl36gDLwLdiXcRWsgqyxSuaChxePXEeuzEtSZbzRhyphenhyphen53-UGFmlXcdb31B8DXVPqnmolOpflKSGB8XjPmgIdnnUv3TiDCsLgA1laKON57Q2MCA/s1600/ring6.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgurrMiNLpG8Sg7NYKWLtt1bjQZbRg9UyRl36gDLwLdiXcRWsgqyxSuaChxePXEeuzEtSZbzRhyphenhyphen53-UGFmlXcdb31B8DXVPqnmolOpflKSGB8XjPmgIdnnUv3TiDCsLgA1laKON57Q2MCA/s1600/ring6.png" height="162" width="640" /></a></div>
<br />
The overall flow of a paragraph is also excellent, with the letters falling into self-symmetric curves and alignments.<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiijjNCcShwOkHN5VEHXxkg4HSVGkGv0N5pWkNGhzolxRSeniI3ZkUS3uEtXbWf_wMgJgQ_iCGTSy-SpIKpwd1cqv1DP7RgYtBvAESRhXGuxFUBD__9sl5UgeHUWH3JiIQZMFNs99436yg/s1600/Text.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiijjNCcShwOkHN5VEHXxkg4HSVGkGv0N5pWkNGhzolxRSeniI3ZkUS3uEtXbWf_wMgJgQ_iCGTSy-SpIKpwd1cqv1DP7RgYtBvAESRhXGuxFUBD__9sl5UgeHUWH3JiIQZMFNs99436yg/s1600/Text.png" height="176" width="640" /></a></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
(This is the first paragraph of Lord of The Rings, converted to Tengwar by just changing the font to my Tengwar Transliteral font.)</div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: left;">
If you are interested in playing with Tengwar text for any kind of design please consider downloading the italic and script versions of the font <a href="https://www.myfonts.com/fonts/zephyris/tengwar-transliteral/">here</a>. These cost a few pounds/dollars/euros.</div>
<div>
<br /></div>
If you are interested in reading Tengwar, or manually translating it, then the excellent “Tengwar Textbook” Chris McKay is available online for free: <a href="http://www.scribd.com/doc/61135121/Tengwar-textbook">Tengwar Textbook</a>.<br />
<br />
There are also excellent simple guides on writing in Tengwar (<a href="http://www.starchamber.com/paracelsus/elvish/elvish-in-ten-minutes.html">like this one</a>), but why do that when you could just download my font and type your name?<br />
<br />
Software used:<br />
<a href="https://inkscape.org/">Inkscape</a>: Glyph design<br />
<a href="http://fontforge.github.io/">Fontforge</a>: Font designUnknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-61603866088885679602015-01-07T14:55:00.004+00:002015-01-07T14:56:09.293+00:00Trypanosome Lego<div class="separator" style="clear: both; text-align: left;">
<a href="http://en.wikipedia.org/wiki/Trypanosoma_brucei">Trypanosomes</a> and <i><a href="http://en.wikipedia.org/wiki/Leishmania">Leishmania</a> </i>are the two tropical parasites that I do most of my research on. These cells seem to have a lot of modularity in controlling their shape, and have quite a lot of flexibility in reshuffling where particular structures (made up of many organelles) sit within the cell.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
The base of the <a href="http://en.wikipedia.org/wiki/Flagellum#Eukaryotic">flagellum</a>, the whip-like tail which the cell uses to swim, is also the site where the cell <a href="http://en.wikipedia.org/wiki/Endocytosis">takes up material from its environment</a> (essentially its mouth) <i>and</i> is linked with the <a href="http://en.wikipedia.org/wiki/Golgi_apparatus">Golgi apparatus</a> (an important organelle in protein processing) <i>and</i> the <a href="http://en.wikipedia.org/wiki/Mitochondrion">mitochondrion</a> (the powerhouse of the cell) <i>and</i> links to the mitochondrial DNA. It turns out <a href="http://jcb.rupress.org/content/206/3/377">reducing the level of just one protein</a> in the cell can cause this entire complex structure to shift its position.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Cells are not quite as flexible as Lego, but it is still impressive that a single protein can have such a large effect on the organisation of a cell.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjkC_jrITFcTZVl3EYjsjOro21erquGhM-SwBQkufigqY87wqJmeWBewtV-Gf7oXl5NtQDQY0nIV0fcJgeo7s0tsyzENvgruI1_8ZHwvXRI7QQHA5spbPYqIaevoVjp6vWjMhb_Eckk4hE/s1600/V2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjkC_jrITFcTZVl3EYjsjOro21erquGhM-SwBQkufigqY87wqJmeWBewtV-Gf7oXl5NtQDQY0nIV0fcJgeo7s0tsyzENvgruI1_8ZHwvXRI7QQHA5spbPYqIaevoVjp6vWjMhb_Eckk4hE/s1600/V2.jpg" height="640" width="452" /></a></div>
Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-15895186247797544252014-12-29T13:23:00.002+00:002015-01-03T14:32:39.387+00:00Forgotten Futures - New York<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFtw9Yjsj_DX1iszFLcvQ7G-HhhsM-ECosbp6GLiMlzMFA2-6j9HfS1NWUluzuRx52O1P-kBXyDd9wGue2lWD52hyQShtAXUF-v-6lQdmjG_Fdy8gMYghMiDz3Maf2NSCqmM0GQEuGhV8/s1600/Combined.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFtw9Yjsj_DX1iszFLcvQ7G-HhhsM-ECosbp6GLiMlzMFA2-6j9HfS1NWUluzuRx52O1P-kBXyDd9wGue2lWD52hyQShtAXUF-v-6lQdmjG_Fdy8gMYghMiDz3Maf2NSCqmM0GQEuGhV8/s1600/Combined.jpg" height="470" width="640" /></a></div>
<br />
What if cities looked like this? The 1920s view of cities of the future was glorious; huge buildings towering into the sky, multi-layer roads, rail and pavements, airships and aircraft, and the bold geometry of art deco.<br />
<br />
Sadly this world never came into existence. But what if it had? What would 1950s New York have looked like? I re-imagined this forgotten future based on the view from the Empire State building towards the Grand Central station and the Chrysler building in a world where the 1920s vision of the future came to be.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://zephyris.deviantart.com/art/Forgotten-Future-New-York-503344424"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgy-6IHMoAKXE2DTEQNScWeLv0hF056yP_NltJgWS1mEJTxC08Y4gtKAFTm-ZHOiE63-_IozY575_s8UzT5QkkXpgCsI-K2w8QR0PAEh_ggq4Tnz3fWcWx2SD9Lf0I8m_IDYQhE7a4ApZk/s1600/NYC_B&W_9_Processed_1600.jpg" height="360" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Software used:</div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://www.blender.org/">Blender</a>: 3D modeling, texturing, rendering, compositing.</div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://www.getpaint.net/">Paint.NET</a>: Final image tweaks.</div>
<a href="https://inkscape.org/">Inkscape</a>: Texture detailing.<br />
<br />
Building a forgotten future; 7 days of 3D modelling in 20 seconds:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdjI3hYh4eCuMTGUvBTdG9U4IPWauEtaJxwRwq6ixZtMpivipzhiKEpyJ9W_-kCgy7hSs3U1RKpiZPi2Oj-c-1ZSUtGhlwl-87rnO2Aaxx9oQAjzDdDc3eee3PYXNlkkeobRaK6D8WKFM/s1600/DrawingHistory.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdjI3hYh4eCuMTGUvBTdG9U4IPWauEtaJxwRwq6ixZtMpivipzhiKEpyJ9W_-kCgy7hSs3U1RKpiZPi2Oj-c-1ZSUtGhlwl-87rnO2Aaxx9oQAjzDdDc3eee3PYXNlkkeobRaK6D8WKFM/s1600/DrawingHistory.gif" height="360" width="640" /></a></div>
<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-52463874906373656572014-12-12T09:36:00.004+00:002014-12-16T08:59:51.736+00:00Tides<span style="font-family: inherit;"><span style="line-height: 19.9999942779541px;">Ocean tides are one of the most amazing but overlooked natural wonders of our planet. As the Earth rotates relative to the sun and the moon, their gravity drags the Earth's water about, raising and lowering it in synchrony with the heavens. The importance of tides reaches further than just surfing, sunbathing and shipping: Tides are the reason the moon is drifting away from the Earth at 3.8 </span><span style="line-height: 19.9999942779541px;">cm per year. Tides allow the formation of beaches with rock pools at low tide, that some biologists argue helped the evolution of early life. Tides (of the atmosphere) are the reason a satellite in a low orbit is more likely to burn up on the side of the Earth nearest or opposite to the moon. Tides even influence the time earthquakes happen.</span></span><br />
<div style="border: 0px; line-height: 19.9999942779541px; margin: 0px; padding: 0px;">
<span style="font-family: inherit;"><br /></span></div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">The explanation of why tides happen is classic high school geography/physics. The gravitational pull of an object is felt more strongly by something close to it. In the case of the Earth, this means that the oceans on the closest side of the Earth to the moon feels a stronger gravitational pull than the Earth as a whole, and the oceans on the far side feel a weaker pull. This means that the oceans on the near side of the Earth are pulled into a bulge (a region of high tide) and the oceans in the far side are also flung outward into a bulge (another region of high tide). This causes high and low tides twice per day. Throw in the similar contribution of the sun's gravitational pull, and it also explains spring tides around the time of the new and full moon.</span><br />
<div style="border: 0px; line-height: 19.9999942779541px; margin: 0px; padding: 0px;">
<span style="font-family: inherit;"><br /></span></div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">Of course this is all a bit of a lie to simplify things. Many places have one high and low tide per day, and a few places even have four. Some places have barely any tide, while others have very large tides where the water level can change by many metres. Why? Because the land gets in the way! It is impossible to have a bulge of water where Africa is, even if the moon was directly over the Sahara. So what does the pattern of tides actually look like?</span><br />
<div style="border: 0px; line-height: 19.9999942779541px; margin: 0px; padding: 0px;">
<span style="font-family: inherit;"><br /></span></div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">Something like this:</span><br />
<span style="font-family: inherit;"><span style="line-height: 19.9999942779541px;"><br /></span>
</span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimX0FOGYYPz8vt3EekI83SLYi1n54UF9pfxildojKcRHHJ5nUURsHzt3p5_QKpzreDEPtJXs33SCPBVQ4UubJ0wmrlsj6A0_6A3Eg7SiCNm-MB-hiaoS42SyvJrES1EeY0jZ-5wXuFApA/s1600/K1M2Ani_180_Opt.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimX0FOGYYPz8vt3EekI83SLYi1n54UF9pfxildojKcRHHJ5nUURsHzt3p5_QKpzreDEPtJXs33SCPBVQ4UubJ0wmrlsj6A0_6A3Eg7SiCNm-MB-hiaoS42SyvJrES1EeY0jZ-5wXuFApA/s1600/K1M2Ani_180_Opt.gif" height="320" width="640" /></span></a></div>
<div style="text-align: center;">
<span style="font-family: inherit;">[Watch in HD on <a href="https://www.youtube.com/watch?v=FeZBOtaATbE&feature=youtu.be">YouTube</a>]</span></div>
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit; line-height: 19.9999942779541px;">This animation shows sea levels over the course of one day, where orange represents high water level, and blue represents low water level. Instead of the water levels changing because of two big bulges of water, there are instead complex patterns of water level change.</span><br />
<div style="border: 0px; line-height: 19.9999942779541px; margin: 0px; padding: 0px;">
<span style="font-family: inherit;"><br /></span></div>
<span style="font-family: inherit;"><span style="line-height: 19.9999942779541px;">So, how does the simple rotation of the Earth relative to the sun and moon generate such complexity? It is easiest to think about the oceans as containers of water which gently slosh about as the water gets pulled by the gravity of the sun and moon. It is a bit like the sloshing of water you get carrying a glass of water, or when you climb out of a bathtub. </span><span style="line-height: 19.9999942779541px;">The precise pattern of the sloshing depends on many things; the strength and direction of the gravitational force driving the sloshing, the depth of the water, and how the oscillating sloshing movement resonates when it gets trapped against the coastline.</span></span><br />
<div style="border: 0px; line-height: 19.9999942779541px; margin: 0px; padding: 0px;">
<span style="font-family: inherit;"><br /></span></div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">The different water movements that make up the final tidal moment can be broken down by the force that generated them (the sun, the moon) and their frequency (once a day, twice a day). The two biggest contributing movements are a twice daily movement arising from the moon, and a once daily movement due to the combined action of the sun and moon.</span><br />
<div>
<span style="font-family: inherit; line-height: 19.9999942779541px;"><br /></span></div>
<div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">These individual movements are mapped through their amplitude (how much the water changes height) and their phase (the relative time of high tide). These maps are surprisingly beautiful! Here are a couple of examples:</span></div>
<div>
<span style="font-family: inherit; line-height: 19.9999942779541px;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlpC7sOBTNeOLHmLfzVNbpRj5cguU7zYpJTDAW4jhTVlnUXEUdAnvuRa_wIKgZLeCTThX6myYyR6WI-Q_z294JlCfkoVe3vUy2k9cs0h33i1frwMEmYjOhZtE55by-uiajFxpgpe1wElQ/s1600/Tide_M2_PhaContoursHue_AmpVal_noise_470.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlpC7sOBTNeOLHmLfzVNbpRj5cguU7zYpJTDAW4jhTVlnUXEUdAnvuRa_wIKgZLeCTThX6myYyR6WI-Q_z294JlCfkoVe3vUy2k9cs0h33i1frwMEmYjOhZtE55by-uiajFxpgpe1wElQ/s1600/Tide_M2_PhaContoursHue_AmpVal_noise_470.png" height="320" width="640" /></span></a></div>
<div>
<span style="font-family: inherit; line-height: 19.9999942779541px;"><br /></span></div>
<div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">These are the patterns of movement of the "M2" part of tides, which is a twice daily water movement arising from the primary action of the moon's gravity. Brightness represents the amplitude, from black (zero amplitude) to white (5 metres amplitude). The coloured lines are a bit more complex. They represent the places where the highest water level occurs due to the M2 tidal component at different times, from red (at 0 hours) through the colours of the spectrum at 1 hour steps.</span></div>
<div>
<span style="font-family: inherit; line-height: 19.9999942779541px;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgey4n3bypLEWmPlQyL0YSf3WmEdNo8EEg_kGdbKgMDnTQs8BNAwP5c3tn9xHcMFlC6hvkPQHxqO140tcmvpesFQWVLPA8vg8Dru1C-5ngr-8AkMskl6no339eovXZeBVu4yoe2eEmMePQ/s1600/Tide_K1_PhaContoursHue_AmpVal_noise_250.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgey4n3bypLEWmPlQyL0YSf3WmEdNo8EEg_kGdbKgMDnTQs8BNAwP5c3tn9xHcMFlC6hvkPQHxqO140tcmvpesFQWVLPA8vg8Dru1C-5ngr-8AkMskl6no339eovXZeBVu4yoe2eEmMePQ/s1600/Tide_K1_PhaContoursHue_AmpVal_noise_250.png" height="320" width="640" /></span></a></div>
<span style="font-family: inherit;"><br /></span>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<span style="font-family: inherit; line-height: 19.9999942779541px;">These are the patterns of movement of the "K1" part of tides, which is a once daily water movement arising from the combined action of the sun's and moon's gravity. Again, brightness represents amplitude, but the amplitudes are smaller and white represents only 2.5 metres. The coloured lines represent the time when highest water level due to the K1 tidal component occur, but this time separated by 2 hour steps.</span><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">These are just the two largest components of tides, there are many complex contributing factors: M2: principal semi-diurnal lunar, S2: principal semi-diurnal solar, N2: larger semi-diurnal elliptical lunar, K2: declinational semi-diurnal solar/lunar, 2N2: second-order semi-diurnal elliptical lunar, K1: principal diurnal solar/lunar, O1: principal lunar, P1: principal diurnal solar, Q1: larger diurnal elliptical lunar. Each of these components has similarly beautiful patterns of movement.</span><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">Software used:</span><br />
<span style="font-family: inherit;"><a href="http://imagej.nih.gov/">ImageJ</a>: <a href="http://icdc.zmaw.de/hamtide.html">HAMTIDE</a> tital data plotting.</span>Unknownnoreply@blogger.com6tag:blogger.com,1999:blog-1382329114149565542.post-17352609007883902382014-11-20T10:36:00.000+00:002014-11-20T10:36:14.223+00:00This one goes out to the cilia biologists... <div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3qFj81X49TW48zyl5mXAHiuBt-jXSKVR5xVBvG2ncchAC3OWyVogNN6nIXnNgCXgKFyWD20Eqn8lYY8guK-oYuHjih7uGIYGuqawmepgOyClAxi9B9pETvpdjCC-_evwelcjQnMxIgKE/s1600/1416475272395_large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3qFj81X49TW48zyl5mXAHiuBt-jXSKVR5xVBvG2ncchAC3OWyVogNN6nIXnNgCXgKFyWD20Eqn8lYY8guK-oYuHjih7uGIYGuqawmepgOyClAxi9B9pETvpdjCC-_evwelcjQnMxIgKE/s1600/1416475272395_large.png" height="420" width="640" /></a></div>
<br />
<br />
Have no idea what this is about? Try reading about <a href="http://en.wikipedia.org/wiki/Cilium">cilia</a> and <a href="http://en.wikipedia.org/wiki/Hedgehog_signaling_pathway">hedgehogs</a>...Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-51373125593792733122014-07-08T13:39:00.000+01:002014-07-09T09:52:45.457+01:003D Wood GrainUsing a block of wood and a plane Keith Skretch made something amazing. He snapped a picture of the wood, then planed a thin layer off, snapped another picture, planed another layer off, and repeated this hundreds of times. In the resulting timelapse/stop motion video you fly through the wood structure, and can see knots and grain in the wood ripple by.
<br />
<br />
<center>
<iframe allowfullscreen="" frameborder="0" height="365" mozallowfullscreen="" src="//player.vimeo.com/video/76973207" webkitallowfullscreen="" width="650"></iframe> <br />
<a href="http://vimeo.com/76973207">Waves of Grain</a> from <a href="http://vimeo.com/user1128836">Keith Skretch</a> on <a href="https://vimeo.com/">Vimeo</a></center>
<center>
</center>
<center style="text-align: left;">
To my computational image analysis eyes, the truly amazing thing about this video is contains the detailed three dimensional map of the internal structure of blocks of wood; that these blocks of wood have been digitally immortalised!</center>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
Let's look at just one of the blocks of wood:</center>
<center style="text-align: left;">
</center>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgL134v8QWtU-GLi7vJNWO3vPEaJXkmjWxbob5gxytyahxUv99hCxyY-IqB9UcF7RSvHdZXmp46GsnIllN4cVkmvjPMizVG2gt0n-gY-_OWS83-2ZY7bX3_h2T9yT5g9d5lXJLTSbbGJdw/s1600/NewStack.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgL134v8QWtU-GLi7vJNWO3vPEaJXkmjWxbob5gxytyahxUv99hCxyY-IqB9UcF7RSvHdZXmp46GsnIllN4cVkmvjPMizVG2gt0n-gY-_OWS83-2ZY7bX3_h2T9yT5g9d5lXJLTSbbGJdw/s1600/NewStack.gif" /></a></div>
<div style="text-align: center;">
The series of images 29-36 seconds through Waves of Grain</div>
<br />
So what can you do with this data? Well you can reproject to give you a virtual view of what the left and the front sides of the blocks of wood would have looked like:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvCWkPoPby2aCWb-QXgEmDibx-tL-URmBW1hFd7czkmUUpvWI0LTMElFoTGevW3ABZhsErA2OsnLXNCHpBnLrW1vK14V4h1bLcK4-9HcGyBauRngVFJlhUPLMTCy3IMU2oyVy5CZqlSjM/s1600/svg.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvCWkPoPby2aCWb-QXgEmDibx-tL-URmBW1hFd7czkmUUpvWI0LTMElFoTGevW3ABZhsErA2OsnLXNCHpBnLrW1vK14V4h1bLcK4-9HcGyBauRngVFJlhUPLMTCy3IMU2oyVy5CZqlSjM/s1600/svg.png" height="464" width="640" /></a></div>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
That's quite cool, but doesn't capture the power of having the full 3D information. The more powerful thing you can do is do a virtual cuts through anywhere you want in the block of wood. You can cut it somewhere in the middle to take a look at the internal structure... The yellow lines mark where the virtual slices were made:</center>
<center style="text-align: left;">
</center>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_YvXNznVrlobSLWbI9lWooCj5ijqqxJPf_tLxlJI7P5P0xP7Ml9W2sMugabZJe4hPJCdAfeBLLtw4scDA2cUbCfy3vBPU-Jr-RPBIb9Uvf7xXyuQjQ_DkhAUrW2YCAxw4RfDpX8cuJFc/s1600/svg.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_YvXNznVrlobSLWbI9lWooCj5ijqqxJPf_tLxlJI7P5P0xP7Ml9W2sMugabZJe4hPJCdAfeBLLtw4scDA2cUbCfy3vBPU-Jr-RPBIb9Uvf7xXyuQjQ_DkhAUrW2YCAxw4RfDpX8cuJFc/s1600/svg.png" height="464" width="640" /></a></div>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
That's also quite cool, but still doesn't capture the power of having all that 3D data. You can also reslice the image at any orientation that you want; it doesn't have to be neat orthogonal lines:</center>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
</center>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqC62T4VBg-6HKBdetnY1Bw2kXe4ogpeKrRHgR1rI63ii5FQFZUQTXrlWfpHkBbf1GHenbWtCwXMAFrEt9AgGLyxrko7KCUishkvfGOCkfnE6QODdLRvllZPvDA9eZVD8AVjaSArDIpPg/s1600/Sectioned_Mod.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqC62T4VBg-6HKBdetnY1Bw2kXe4ogpeKrRHgR1rI63ii5FQFZUQTXrlWfpHkBbf1GHenbWtCwXMAFrEt9AgGLyxrko7KCUishkvfGOCkfnE6QODdLRvllZPvDA9eZVD8AVjaSArDIpPg/s1600/Sectioned_Mod.png" height="531" width="640" /></a></div>
<br />
Again, quite cool. But you can still do more. Because this is now a purely digital representation of this block of wood you can display it in ways that would be physically impossible to make. Instead of just looking at the outside of the block...<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhccAtK21pq77QKrG_p4jLG_B9ITzi-YYJXw8uOVyGC2BWAta5JEpNeVHCmcpocI2wPCvBMYQv4gc3J-C1oXf-xpKmrbyDpfsSnSbhlDOiRaZQIAcBAtJpjpGjGhBbbYNMjCCJpzbyKxjo/s1600/Renders_Crop1_mod.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhccAtK21pq77QKrG_p4jLG_B9ITzi-YYJXw8uOVyGC2BWAta5JEpNeVHCmcpocI2wPCvBMYQv4gc3J-C1oXf-xpKmrbyDpfsSnSbhlDOiRaZQIAcBAtJpjpGjGhBbbYNMjCCJpzbyKxjo/s1600/Renders_Crop1_mod.png" height="472" width="640" /></a><br />
<br />
... you can now look inside.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjU-Ej826gTbla-86vNYJp06lRlwc8qDdvxjCIfWBw0iWEGwLflY1zHV3yqN5Gh3sw8vpj4nG0hoA-a9oHp5OiDhlh1Sb1ZhOnNoZdLSx1oPXg3Mky0IdfO-sgdT5IDohshTyNrQNYQIhM/s1600/Renders_Crop2_mod2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjU-Ej826gTbla-86vNYJp06lRlwc8qDdvxjCIfWBw0iWEGwLflY1zHV3yqN5Gh3sw8vpj4nG0hoA-a9oHp5OiDhlh1Sb1ZhOnNoZdLSx1oPXg3Mky0IdfO-sgdT5IDohshTyNrQNYQIhM/s1600/Renders_Crop2_mod2.png" height="472" width="640" /></a><br />
<br />
This 3D reconstruction lets you see how the growth rings appear in three dimensions, showing exactly where the grain runs. It lets you see how the knot, which is where a branch grew from the tree, cuts through the growth rings in a distinctive way. It lets you see pretty much everything about the internal structure of the wood!<br />
<br />
This kind of approach is used all over biology, and is normally called something like serial sectioning. You can use it for everything from reconstructing a <a href="https://www.youtube.com/watch?v=dPPjUtiAGYs&hd=1">whole person</a> by histology and a light microscope to a single cell by <a href="http://www.zeiss.co.uk/microscopy/en_gb/products/fib-sem-instruments.html">electron microscopy</a>.<br />
<br />
Software used:<br />
<a href="http://imagej.nih.gov/ij/">ImageJ</a>: 3D reconstructions<br />
<center style="text-align: left;">
</center>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
</center>
<center style="text-align: left;">
</center>
Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-1382329114149565542.post-90290313514333055512014-07-03T16:45:00.004+01:002014-07-03T16:53:38.278+01:003D Lightning 2About a year ago two redditors happened to take a photo of the same lightning bolt, but from different places, and I use them to make a 3D reconstruction: <a href="http://calculatedimages.blogspot.co.uk/2013/05/3d-lightning.html">3D Lightning</a>.<br />
<br />
Well, <a href="http://www.reddit.com/r/pics/comments/29pyrx/two_redditors_take_the_same_picture_at_the_same/">it happened again</a>!<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiCjV7SL1H4EuzWfjGQxCywCcNmcP_YAf_iEEG55hW1igGT2C3eIjcaL8V-YtzVlltWes4EcL1AyXUQuujnmmg-gi5hQ7usjEc8s6Evdv1Qa0pNArBFOOqbewSeL-sSYX4prANf2-Ik5Ek/s1600/PDXykys.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiCjV7SL1H4EuzWfjGQxCywCcNmcP_YAf_iEEG55hW1igGT2C3eIjcaL8V-YtzVlltWes4EcL1AyXUQuujnmmg-gi5hQ7usjEc8s6Evdv1Qa0pNArBFOOqbewSeL-sSYX4prANf2-Ik5Ek/s1600/PDXykys.jpg" height="640" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
The two source images.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
This time the lightning bolt struck one World Trade Center (Freedom Tower), and two people got a shot of it from over the river. A little adjustment for the rotation of the image and some guestimation of their approximate locations let me work out that there was very little vertical shift between their locations, but quite a large horizontal shift.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Just like last time, a 100% accurate reconstruction isn't possible. You need to know the exact locations and elevations of the people, and field of view of the cameras used, to do this precisely. However, just like last time, a rough reconstruction is possible where the difference in horizontal position of part of the lightning bolt between the two images is proportional to the distance from the people taking the photos.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaM3Ai3k0xWjz46UWZD0pGsrrG8lPAM0q1nDxRmcAA3TF_8DuCmvJ6XHwowPnulmxKYBd1fm6isSCy5iYPO5yg0y_1pjvfsiJWOshqIzDoYmpKOlBfKDyQAruqUU1AwW-e2CbPb_IxOqM/s1600/CombinedTif_Ani.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaM3Ai3k0xWjz46UWZD0pGsrrG8lPAM0q1nDxRmcAA3TF_8DuCmvJ6XHwowPnulmxKYBd1fm6isSCy5iYPO5yg0y_1pjvfsiJWOshqIzDoYmpKOlBfKDyQAruqUU1AwW-e2CbPb_IxOqM/s1600/CombinedTif_Ani.gif" height="640" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
The approximate 3D reconstruction.</div>
<br />
After grabbing the coordinates from the photos it was just a matter of plugging them into Blender to make an approximate 3D reconstruction.<br />
<br />
<div class="separator" style="clear: both;">
Software used:</div>
<div class="separator" style="clear: both;">
<a href="http://rsbweb.nih.gov/ij/">ImageJ</a>: Image analysis.</div>
<div class="separator" style="clear: both;">
<a href="http://www.blender.org/">Blender</a>: 3D modelling and rendering.</div>
Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-1382329114149565542.post-18586865272069455732014-06-08T17:34:00.001+01:002014-06-08T17:35:57.656+01:00PixelToolMany classic games like <a href="https://en.wikipedia.org/wiki/Transport_Tycoon">Transport Tycoon</a>, <a href="https://en.wikipedia.org/wiki/RollerCoaster_Tycoon">Rollercoaster Tycoon</a> and <a href="https://en.wikipedia.org/wiki/Theme_Hospital">Theme Hospital</a> have pixel art graphics using a limited number of colours. These graphics are tricky to draw and take a lot of skill, especially when trying to draw accurate 3D shapes from different angles and getting the perspective and shading right.<br />
<br />
So I made <a href="http://www.richardwheeler.net/interactive/pixeltool.html">PixelTool</a> to help out!<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjftWnrPNuYUtcr7aLGUKSBKRYsxVM3uSTzV5fFbU-hH6g05eSjTWfwCD6U4oWDgQZ1GZrC3aD4WLZLL_K8MzsD0JzhYURHtQi1i6vl_lQ_WCyLcAS_C8GtwiYGYnpWXzmE9PmM8Hsm__M/s1600/Screenie.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjftWnrPNuYUtcr7aLGUKSBKRYsxVM3uSTzV5fFbU-hH6g05eSjTWfwCD6U4oWDgQZ1GZrC3aD4WLZLL_K8MzsD0JzhYURHtQi1i6vl_lQ_WCyLcAS_C8GtwiYGYnpWXzmE9PmM8Hsm__M/s1600/Screenie.png" height="374" width="640" /></a></div>
<br />
<br />
What is PixelTool?<br />
<br />
PixelTool is an online <a href="https://en.wikipedia.org/wiki/Voxel">voxel</a>-based tool for drawing isometric pixel art graphics. To use it you modify a 3D volume of voxels; picking 8-bit colours for each of the voxels and leaving the background as the 'magic blue' which is transparent.<br />
<br />
It takes the voxel data and does a pixel-perfect rendering of it into 3D and adding lighting and shadowing, but still sticking to the starting 8-bit colour palette.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEinUSTGrhWejMIzIJqB2K-YJllVLmMj-g8rWAjWbHG7r8JQ-X2xK2draexmpRiMKP9oVYq6iFgyapUqrUB970AKDcS8EwPWq_T42D012FLPqux9I8PcDfhuZLoC9xwAnyxlNdmnaK9H7s0/s1600/Voxels.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEinUSTGrhWejMIzIJqB2K-YJllVLmMj-g8rWAjWbHG7r8JQ-X2xK2draexmpRiMKP9oVYq6iFgyapUqrUB970AKDcS8EwPWq_T42D012FLPqux9I8PcDfhuZLoC9xwAnyxlNdmnaK9H7s0/s1600/Voxels.png" height="374" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">Slices through the voxel data of a piece of heavy hauling equipment for <a href="http://www.openttd.org/">OpenTTD</a></span></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPIPUreghreriXV0l13W58PbToGPhDLJA3bovd5SXiEqWBh7StB9sJOPvPzZxoVE7QdKTz_gOXHRsSWh5gNa8LvNbisnWoar7mXD1aLSD2Cxb7qr_5lfSFrZFwUfkBo1rcqX4pLMULiF8/s1600/RenderedSmall.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPIPUreghreriXV0l13W58PbToGPhDLJA3bovd5SXiEqWBh7StB9sJOPvPzZxoVE7QdKTz_gOXHRsSWh5gNa8LvNbisnWoar7mXD1aLSD2Cxb7qr_5lfSFrZFwUfkBo1rcqX4pLMULiF8/s1600/RenderedSmall.png" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">The corresponding rendered image of the voxel block.</span></div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Blowing up the voxels in the rendered image by 4 times lets you see what is going on in a bit more detail:</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqI-rVfY_GjMqCKzlVHDcPOGidLFILurkV9V7IBKb-uv923XnmU1mkclyfBq1Ksd4vMlACRrKDkh8IDO_lpz23lk9qGB-29igWF9z6aB4dYSw9zIJWcgR58bs60zEKsrFNpN2ea2DtoQ8/s1600/Rendered.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqI-rVfY_GjMqCKzlVHDcPOGidLFILurkV9V7IBKb-uv923XnmU1mkclyfBq1Ksd4vMlACRrKDkh8IDO_lpz23lk9qGB-29igWF9z6aB4dYSw9zIJWcgR58bs60zEKsrFNpN2ea2DtoQ8/s1600/Rendered.png" height="86" width="640" /></a></div>
<br />
PixelTool isn't just a cheap imitation of 3D rendering software, it is a dedicated tool streamlined to making isometric sprites for classic 8-bit games.<br />
<br />
Want to play some more?<br />
Test PixelTool out online here: <a href="http://www.richardwheeler.net/interactive/pixeltool.html">http://www.richardwheeler.net/interactive/pixeltool.html</a><br />
Grab the source HTML/javascript code here: <a href="http://dev.openttdcoop.org/projects/pixeltool">http://dev.openttdcoop.org/projects/pixeltool</a><br />
Download this example of voxel data here: <a href="http://www.richardwheeler.net/hosting/voxeldata.txt">www.richardwheeler.net/hosting/voxeldata.txt</a><br />
Join the discussion here: <a href="http://www.tt-forums.net/viewtopic.php?f=26&t=69974&start=60">http://www.tt-forums.net/viewtopic.php?f=26&t=69974&start=60</a><br />
<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1382329114149565542.post-68965586765746941972014-05-20T00:27:00.000+01:002014-05-20T00:27:18.955+01:00Jurassic Wedding<div class="separator" style="clear: both; text-align: center;">
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSHDIdKLN9170NmbJ-mBUjU_oQPA4pC-C3av5Up7ok_w8QUOGddNxzmYHJFLSpv9yNdXq4vTIvp4TyJ9emZpt1LTneLEbnxMZASCLAyDixZvwwy58D9riXW_FpRBvv-RBAqMkGwSryOxk/s1600/140405suri543_trex2_rerender.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSHDIdKLN9170NmbJ-mBUjU_oQPA4pC-C3av5Up7ok_w8QUOGddNxzmYHJFLSpv9yNdXq4vTIvp4TyJ9emZpt1LTneLEbnxMZASCLAyDixZvwwy58D9riXW_FpRBvv-RBAqMkGwSryOxk/s1600/140405suri543_trex2_rerender.png" height="426" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
You will have seen the instant internet classic of a <a href="http://www.huffingtonpost.com/2013/05/30/dinosaur-wedding-photo-_n_3360438.html">dinosaur crashing a wedding</a>... I got married this year and just had to do the same. Fortunately my wife agreed! I am a biochemist, but cloning a dinosaur to crash my wedding would have been a bit of a challenge, so I had to stick to the graphics approach instead.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
So how do you get a dinosaur to crash your wedding?</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Step 1: Recruit an understanding wedding photographer and guests for a quick running photoshoot. Make sure everyone is screaming and staring at something imaginary!</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJ6dXE0L_ByzT3pkllhKLMbsPfwgC0_pljX6JIxcZs6i5VTQykP5tIpzJCsuv3RPSB8CUkJCCVEiQmW2yQ4ZUIB37Y68jUP5J8iTl7vgt2q1JH1dVs2j4mBm-wr1NS6WaT8Jte1yyizhs/s1600/140405suri543.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJ6dXE0L_ByzT3pkllhKLMbsPfwgC0_pljX6JIxcZs6i5VTQykP5tIpzJCsuv3RPSB8CUkJCCVEiQmW2yQ4ZUIB37Y68jUP5J8iTl7vgt2q1JH1dVs2j4mBm-wr1NS6WaT8Jte1yyizhs/s1600/140405suri543.jpg" height="425" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Step 2: Recruit a dinosaur. A virtual one will do, and I used <a href="http://www.blendswap.com/blends/view/2792">this</a> excellent freely available <i>Tyrannosaurus rex </i>model for blender.</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGJLVV8mHKvFRVtohqntSJxUseW8myhLkcPU-rZF5fMb4VsFFdSk6VKjdubQn3HZ3YbCqhyphenhyphennFu9neELhqEBc_uSXM3JCY3bw4RA43GOJtqfw62fnY_IQ5jfpD4jc02QZmW9ts2Ha70OF0/s1600/Rex_Model.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGJLVV8mHKvFRVtohqntSJxUseW8myhLkcPU-rZF5fMb4VsFFdSk6VKjdubQn3HZ3YbCqhyphenhyphennFu9neELhqEBc_uSXM3JCY3bw4RA43GOJtqfw62fnY_IQ5jfpD4jc02QZmW9ts2Ha70OF0/s1600/Rex_Model.png" height="238" width="400" /></a></div>
<br />
<br />
<div class="separator" style="clear: both; text-align: left;">
Step 3: Get some dynamic posing going on! Most 3D graphics software uses a system called 'rigging' to add bones to a 3D model to make it poseable. This is exactly what I did, and with 17 bones (three for each leg, seven for the tail, two for the body and neck and two for the head and jaw) I made our pet <i>T. rex </i>poseable.</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbr2n5ob50KwexgejZ9wZyHVeN5P6I9_jXeEgdAQd2OTm2GaszkTYrvkJvYH1LlP4TtrZ-COs0m0qFn8bO59x8KC-TnV2sKryqY1jrQQJAK8aFInih-FPQA8pv9AAokFeq9CEowEN8BO0/s1600/Rex_Bones.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbr2n5ob50KwexgejZ9wZyHVeN5P6I9_jXeEgdAQd2OTm2GaszkTYrvkJvYH1LlP4TtrZ-COs0m0qFn8bO59x8KC-TnV2sKryqY1jrQQJAK8aFInih-FPQA8pv9AAokFeq9CEowEN8BO0/s1600/Rex_Bones.png" height="238" width="400" /></a></div>
<div style="text-align: center;">
<span style="font-size: xx-small;">The bone system</span></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikXRScKCnlOb8OX9SOHTR46wr_vYobZMbWenG37FvEptcR8AcTtbstpXhaHwnikfl85c0OdQPTFK86HBSYtgENb06j0xEhFK4jA4_MIZ0q_Vz_lCGdNIeEjGNqnpkydMFBycmaHHjgBtg/s1600/Rex_Posed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikXRScKCnlOb8OX9SOHTR46wr_vYobZMbWenG37FvEptcR8AcTtbstpXhaHwnikfl85c0OdQPTFK86HBSYtgENb06j0xEhFK4jA4_MIZ0q_Vz_lCGdNIeEjGNqnpkydMFBycmaHHjgBtg/s1600/Rex_Posed.png" height="238" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">The posed result</span></div>
<br />
<div class="separator" style="clear: both; text-align: left;">
Step 4: Get the <i>T. rex</i> into the scene. By grabbing the EXIF data from the running photo I found that it was shot with a 70mm focal length lens. By setting up a matching camera in blender and tweaking its position I made the camera position match perspective between the view of the <i>T. rex</i> and the running people.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJJOOre3kSMbyYPqfoS3sksGBFbieOWLdoVkWjUTH1FE0gY4QNbxzrzfvMaJZNub9mlGrnMn0vnIn2rF-lmRxIxEh3JIpt6R8eG_-wGgC94aPBY94S7KdGTiK1GILBL4i4rZWB2I9pyfs/s1600/PerspectiveMatch.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJJOOre3kSMbyYPqfoS3sksGBFbieOWLdoVkWjUTH1FE0gY4QNbxzrzfvMaJZNub9mlGrnMn0vnIn2rF-lmRxIxEh3JIpt6R8eG_-wGgC94aPBY94S7KdGTiK1GILBL4i4rZWB2I9pyfs/s1600/PerspectiveMatch.png" height="448" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Step 5: Making the dino look good. A 3D model is just a mesh of points in 3D space. To get it looking good texturing and lighting need to be added. For this project they also need to match the photo. Matching the lighting is particularly important, and I used Google maps and the time the photo was taken to match up where the sun was as accurately as possible.</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiooswESLXyAzHkwwKOAkRtRbroh0I352SW130c7n-XtRvxi-6VnaPcmES48etqLh9f-NUsHQudHxjnAmxoa-zH9GEVGbYwCgK7eI04R2KIVN7mW2Hg7rdbLdVQjoBId-WAUA7lbw1VRNg/s1600/Render_Wireframe.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiooswESLXyAzHkwwKOAkRtRbroh0I352SW130c7n-XtRvxi-6VnaPcmES48etqLh9f-NUsHQudHxjnAmxoa-zH9GEVGbYwCgK7eI04R2KIVN7mW2Hg7rdbLdVQjoBId-WAUA7lbw1VRNg/s1600/Render_Wireframe.png" height="266" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">The <i>T. rex </i>wireframe</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPJ7LlQ4Wcsh5u1Bbpl1rUVRc6fyQ4uzY9EmQJpDZ0V6BPe48DWlRnyYEnDTsmBK7VKem9EmlDJmImFeXz3bWlyxwTlbXn3NKKWYDskOg2enzx3Y9FlAITXDuyCZP5NiClYzp4mouW4Jk/s1600/Render_Untextured.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPJ7LlQ4Wcsh5u1Bbpl1rUVRc6fyQ4uzY9EmQJpDZ0V6BPe48DWlRnyYEnDTsmBK7VKem9EmlDJmImFeXz3bWlyxwTlbXn3NKKWYDskOg2enzx3Y9FlAITXDuyCZP5NiClYzp4mouW4Jk/s1600/Render_Untextured.png" height="266" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">Textured with a flat grey texture.</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;"><br /></span></div>
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqGY1t23Zs-SszrVtSoQsSPylxhxu1XA-JoLdZny7oPPJJgN_7UwKXTd7nAgy8OPVwDDeoHjyZEyWLAxH9tz5G99fzJruyYhtuTwZ_KAAgtrLz4v_8FK9Mi_0wYnX7zEOX0XXjzi69Who/s1600/Render_DetailTexture.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqGY1t23Zs-SszrVtSoQsSPylxhxu1XA-JoLdZny7oPPJJgN_7UwKXTd7nAgy8OPVwDDeoHjyZEyWLAxH9tz5G99fzJruyYhtuTwZ_KAAgtrLz4v_8FK9Mi_0wYnX7zEOX0XXjzi69Who/s1600/Render_DetailTexture.png" height="266" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">With a detail bump texture and accurate lighting.</span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2S3Hv8s55V6mQIOYJ19x_tSHr2hcVCJ5OA3iB5lJfNwX_OQov8YEuQzv6c6ZY6CKeuHwh4CF59nW8042SMmk1mrNx1urziM08No42sfz7KmHxB75mpJB-SCUkytIbRk1iKDaTU65pogw/s1600/Render_FullTexture.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2S3Hv8s55V6mQIOYJ19x_tSHr2hcVCJ5OA3iB5lJfNwX_OQov8YEuQzv6c6ZY6CKeuHwh4CF59nW8042SMmk1mrNx1urziM08No42sfz7KmHxB75mpJB-SCUkytIbRk1iKDaTU65pogw/s1600/Render_FullTexture.png" height="266" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: xx-small;">With colours, detail texture and lighting.</span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
Step 6: Layering it all together. To fit into the scene the dinosaur must sit into the picture in 3D; in front of some object and behind others. To do this I just made a copy of some of the guests which need to sit in front of the dinosaur and carefully cut around them. The final result is then just layering the pictures together.<br />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrlISfqmytUHCb2LZBNnkWe_771hxNNwADIsIot6O9LV2fv836Lw_I-ZH1rI0jZRnD0SGDM6gQZOXcRMCAwE-ZGLCneFh76uXY2PRoHG3STW4_kufykYFNubDhlt1ZnGBiugwMU_JZ_iU/s1600/Layers.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrlISfqmytUHCb2LZBNnkWe_771hxNNwADIsIot6O9LV2fv836Lw_I-ZH1rI0jZRnD0SGDM6gQZOXcRMCAwE-ZGLCneFh76uXY2PRoHG3STW4_kufykYFNubDhlt1ZnGBiugwMU_JZ_iU/s1600/Layers.png" height="400" width="640" /></a></div>
<br />
So there you go! 6 steps to make your own wedding dinosaur disaster photo!<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7iBkWCZnfa9x8bn0V78NOh5J-27PuDshVEiCYF5HX6899MwJGqsKJWqZHFaHySvNiA_H1yp5vA4BboRQcogEkOftR-kqzwBfmhHoyXT7OccDWPBjWhlDzaOfjYtlArKQgtSbc2Aq48nY/s1600/140405suri543_trex2_rerender.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7iBkWCZnfa9x8bn0V78NOh5J-27PuDshVEiCYF5HX6899MwJGqsKJWqZHFaHySvNiA_H1yp5vA4BboRQcogEkOftR-kqzwBfmhHoyXT7OccDWPBjWhlDzaOfjYtlArKQgtSbc2Aq48nY/s1600/140405suri543_trex2_rerender.png" height="425" width="640" /></a></div>
<div>
<br /></div>
<div>
Software used:</div>
<div>
<a href="http://www.blender.org/">Blender</a>: 3D modelling and rendering.</div>
<div>
<a href="http://www.getpaint.net/">Paint.NET</a>: Final layering of the image.</div>
Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-1382329114149565542.post-54387718979886380932014-04-28T23:15:00.002+01:002014-04-29T22:59:09.482+01:00A Year in The Life of a Computer<div class="separator" style="clear: both; text-align: left;">
What does a year in the life of a computer look like?</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFByx80oBa7dJlnKAyOFItGiXYNBU7nEknkqxhyphenhyphenJ6QEIYhztNEAcGoPsZF7_Vf2bzzbotHyoij-6ODwTQZQ0ZSKAmdm4Zllp85tgfrHrGkRdrsg03w4EK6j5GX1hjbS2b50ZiBAFwJG60/s1600/IMG_9621_small_levels.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFByx80oBa7dJlnKAyOFItGiXYNBU7nEknkqxhyphenhyphenJ6QEIYhztNEAcGoPsZF7_Vf2bzzbotHyoij-6ODwTQZQ0ZSKAmdm4Zllp85tgfrHrGkRdrsg03w4EK6j5GX1hjbS2b50ZiBAFwJG60/s1600/IMG_9621_small_levels.jpg" height="426" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Well, something like the map below! This is a map every bit of of mouse movement, every mouse click and every keyboard press I have done on my home and work computer over every day of a whole year.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpthlYW0U5mH7ulwFkKpkqtTcng2KFfYGSHScAbPxJKLzcoEMpLHqGS3jJHmi7z93CjH5a4Xi_ivHn34FQyIc3psDRtbR-rHDhS19q273MTAOhBm0vs9D9UsxixpPgu9UU0KhjtHenIc4/s1600/AllLogPlot_Combined_2013_notrans_inv.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpthlYW0U5mH7ulwFkKpkqtTcng2KFfYGSHScAbPxJKLzcoEMpLHqGS3jJHmi7z93CjH5a4Xi_ivHn34FQyIc3psDRtbR-rHDhS19q273MTAOhBm0vs9D9UsxixpPgu9UU0KhjtHenIc4/s1600/AllLogPlot_Combined_2013_notrans_inv.png" height="374" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
2013-2014 [click for a bigger view]</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
To make it I wrote a little python script using pyHook to grab inputs in Windows, which I compiled to an .exe using py2exe. I set this up so that it starts recording the mouse movement, clicks, and keyboard presses after I log into my home or work computer. After 2 years it had collected nearly 10 Gb of data! This was far too much to look through by hand, so I wrote a second set of scripts to plot it to an image.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
So what does it all mean? Well the map breaks down a bit like a normal calendar, with days of the week running from the top to the bottom of the map, and successive weeks running from left to right. The years and months are marked at the top of the map.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhM1UmDvfjcLntB5FzG5GRDydTyez7zSEP08yvqaogheSRTr8Tm_4p1HcGdjwV-mN8U_7RQY5rREdgK5nxQLytFRNv_xZgLzyABAc-tHQFyyz_vqkddvn9CKgLf7EKNhZCZjBFEQtlQzhg/s1600/AllLogPlot_Combined_Key_notrans_inv.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhM1UmDvfjcLntB5FzG5GRDydTyez7zSEP08yvqaogheSRTr8Tm_4p1HcGdjwV-mN8U_7RQY5rREdgK5nxQLytFRNv_xZgLzyABAc-tHQFyyz_vqkddvn9CKgLf7EKNhZCZjBFEQtlQzhg/s640/AllLogPlot_Combined_Key_notrans_inv.png" height="374" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Within each day my computer activity is broken down by time. Time runs from the top to the bottom of each day, from midnight to midnight. Coloured speckles on the dark background indicate computer activity. It is easy to see that I use computers <i>a lot</i>, with a chunk of time from around midnight to 7 am when I am normally asleep, then smatterings of activity from around 8 am to midnight when I am at work or awake at home.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiR3i3bIiFLfoqZcUCkIiKipbPVx-NLm8iGN6HXAf3Y6cKlxU3l2DwYaIpG9HBZssjfXrkDIV_claWU9dKav77RVh34Tow7mOrRy813k2yi5FDt74HR3sxE0eiBUcldaaAqhJVwskRKS_w/s1600/DayKey_notranspinv.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiR3i3bIiFLfoqZcUCkIiKipbPVx-NLm8iGN6HXAf3Y6cKlxU3l2DwYaIpG9HBZssjfXrkDIV_claWU9dKav77RVh34Tow7mOrRy813k2yi5FDt74HR3sxE0eiBUcldaaAqhJVwskRKS_w/s1600/DayKey_notranspinv.png" height="400" width="300" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Different types of computer activity are shown in different colours.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieHHXr_HXGcdwP3KgaNUQgq72xyaHqmyeKjlMK8T5zy7YkljA00pcg34EEID-nXr86yomLc1rCsLd5iiY8FewdJ8Z6RX2tJeMtr10I4X6s41rSL4T4iP0FawUJ_B4SqKWgR-SN_FNjNqw/s1600/DayKey_notrans_inv.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieHHXr_HXGcdwP3KgaNUQgq72xyaHqmyeKjlMK8T5zy7YkljA00pcg34EEID-nXr86yomLc1rCsLd5iiY8FewdJ8Z6RX2tJeMtr10I4X6s41rSL4T4iP0FawUJ_B4SqKWgR-SN_FNjNqw/s1600/DayKey_notrans_inv.png" height="640" width="314" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
The structure within each of the colours also contains information; distance in the horizontal direction corresponds to horizontal mouse position across my two screens (for mouse movement) which mouse button was clicked (for mouse clicks) and which key was pressed (for keyboard presses).</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZfxmowdlzG8hSqFP-Of-Yq1xGfqgXg0b6HKHjCLy2VoQxhNdaRo1nRxrBZjDlhyphenhyphenlurMMQVXeq1437Mzw1Sfl9WiwHDrXm_u0Ix7MD9xKub8TsIrIYU3NBaSylchNxkRIriqKuWiqSXK4/s1600/AllLogPlot_Combined_notrans_inv.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZfxmowdlzG8hSqFP-Of-Yq1xGfqgXg0b6HKHjCLy2VoQxhNdaRo1nRxrBZjDlhyphenhyphenlurMMQVXeq1437Mzw1Sfl9WiwHDrXm_u0Ix7MD9xKub8TsIrIYU3NBaSylchNxkRIriqKuWiqSXK4/s640/AllLogPlot_Combined_notrans_inv.png" height="374" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
2012-2013 [click for a bigger view]</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
In these maps of usage some interesting structures jump out; you can spot the type of work I was doing with my computer based on the type of mouse and keyboard activity:</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjufr5lSYEK81PnCy1db5QOGjb-D-BxKsIYRh2X7gmVs1Hno7VI43ImVgNPeSLLuPxXLvFye_3F7e7u8J8K5GBKpX2wyET6dhf3r4bwaFRONz3LKxuc_HF9dalHuqpyiMzqPNd6qqlcVA4/s1600/June12th2012.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjufr5lSYEK81PnCy1db5QOGjb-D-BxKsIYRh2X7gmVs1Hno7VI43ImVgNPeSLLuPxXLvFye_3F7e7u8J8K5GBKpX2wyET6dhf3r4bwaFRONz3LKxuc_HF9dalHuqpyiMzqPNd6qqlcVA4/s1600/June12th2012.png" height="320" width="80" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
This is usage on a day where I was writing my PhD thesis. The keyboard (cyan) has loads of activity, while the mouse (magenta) did relatively little.</div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhV6ZmoDqw41YpW47UTT7KUNv0rOU8uMJW4_p3CMUlK5cMdIhVgV_PZ_jhg1FDxsqMR-wHysVo1vA9jJ-aBQEV3k_WtPH-m-J0O8uL4rW9TQKlnvHzBWlj0o-3KGb3v3yXhlpagDh2epd0/s1600/March16th2013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhV6ZmoDqw41YpW47UTT7KUNv0rOU8uMJW4_p3CMUlK5cMdIhVgV_PZ_jhg1FDxsqMR-wHysVo1vA9jJ-aBQEV3k_WtPH-m-J0O8uL4rW9TQKlnvHzBWlj0o-3KGb3v3yXhlpagDh2epd0/s1600/March16th2013.png" height="320" width="80" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
This is a day where I was mainly using Blender for 3D graphics. The mouse (magenta) has huge levels of activity, centred on just the left hand screen). The keyboard is hardly active except for the control and shift keys, which light up as a single column of bright cyan pixels.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
It is quite scary how much information can be gleaned from these maps of computer activity. Without knowing which programs were open or which keyboard keys were being pressed it is still easy to work out where I have been, when I have been working, and the kind of things I was doing on my computer. Similar data can be collected remotely; particularly if an internet company tracks when and where you use the internet.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Stop for a second and think about the companies you interact with, and the data mining they can do. Think how much they can learn about you and your habits; Google and the websites you visit, your phone company and when and who you text and call, the supermarket you shop in and what you buy. These companies can work out what you are interested in, what you like and dislike, when you are awake and when you are asleep. This is <a href="https://en.wikipedia.org/wiki/Big_data">big data</a>, and it is valuable and it is powerful. Big data is how <a href="http://www.forbes.com/sites/kashmirhill/2012/02/16/how-target-figured-out-a-teen-girl-was-pregnant-before-her-father-did/">Target knew a man's teenage daughter was pregnant before he did</a>!</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Software used:</div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://sourceforge.net/apps/mediawiki/pyhook/index.php?title=Main_Page">pyHook</a> and <a href="http://www.py2exe.org/">py2exe</a>: Data logging.</div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://imagej.nih.gov/ij/">ImageJ</a>: Data plotting.</div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://www.inkscape.org/en/">Inkscape</a>: Plot annotation.</div>
Unknownnoreply@blogger.com1