Difference between revisions of "Team:Cambridge-JIC/Notebook"

graph.merge('enose', 'meta', '', $('<div style="margin-top:-40px"><h4>General</h4> Bionose project ended. Check out <a href= "http://www.owlstonenanotech.com" class="blue">OwlStone</a> (Cambridge based company): their chemical sensing technology is amazing!</div>'));

graph.commit('optics', 'Optics', $('<div>15 July 2015: Designing optical bench system to test our potential components of the microscope. We ran out of 3D printing material :( but had insightful talks by Prof. Clemens Kaminski and Dr. Filipe Lourenco on Fluorescence and Super-resolution imaging.</div>'));

graph.commit('sw', 'Software', $('<div>16 July 2015: Autofocus and microscope control software already available in Python open-source. Plan to make it more streamlined and user-friendly.</div>'));

graph.commit('optics', 'Optics', $('<div>16 July 2015: Got tips on designing an Epifluorescence optical pathway from Dr Richard Bowman.</div>'));

graph.commit('design', 'Hardware Design', $('<div>17 July 2015: Printed the new upright stage, with x- and y-axis translation systems. Also made some lens holders for our optics bench. Simon loves printing.</div><div class="teamen"><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/b/b1/CamJIC-Notebook-Optics3.jpg)"><div class="blur"></div><div class="profile"><h3>Optics</h3><p>Some filters arrived today. These are typically used for photography - put in front of the camera flash. But we are trying to find out (using a spectrophotometer) whether they could be good enough to incorporate in a fluorescent microscope. Collecting filter specs with a spectrophotometer and plotting in MatLab.</p></div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/6/6f/CamJIC-Notebook-Optics1.jpg)"><div class="blur"></div><div class="profile"><h3>Optics & Hardware</h3><p>Simon testing his freshly printed lens holder. We came up with the idea to use a magnetic whiteboard as a substitute of an optical table worth thousands of pounds. It is all about the open source cheap stuff now!</p></div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/8/8d/CamJIC-Notebook-Optics2.jpg)"><div class="blur"></div><div class="profile"><h3>Optics</h3><p>The resolution which can be achieved with a single lens with a short focal distance is amazing: the individual plastic fibres of the 3D printed parts are easily visible.</p></div></div></div>'));

graph.commit('optics', 'Optics', $('<div>20 July 2015: First prototype working. Very cheap, very poor quality… but we are working on it. The inverted-lens Raspberry Pi Cam definitely gives decent resolution, with its NA of about 0.15. Excited to see some cheek epidermis cells. Or maybe something else… Anyways excited!!!</div> <div class="teamen"><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/4/46/CamJIC-Notebook-Optics4.jpg)"><div class="blur"></div><div class="profile"><h3>Microscope</h3><p>The first image obtained with our microscope. Featuring a sample of epidermis from one of our team members. Thank you, Atti.</p></div></div> <div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/e/e9/CamJIC-Notebook-Optics5.jpg)"><div class="blur"></div><div class="profile"><h3>Microscope</h3><p>The first prototype in its whole glory.</p></div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/3/3b/CamJIC-Notebook-Software1.jpg)"><div class="blur"></div><div class="profile"><h3>Software</h3><p>Face recognition working! Cell recognition coming soon.</p></div></div></div>'));

graph.commit('sw', 'Software', $('<div>20 July 2015: Playing around with some face recognition software. If we can digitally recognise faces, we could possibly also recognise cells, right?</div>'));

graph.commit('design', 'Hardware Design', $('<div>20 July 2015: Currently designing and 3D printing some more holders for the optical bench setup. Just found out that OpenSCAD is not as easy to manipulate with as it seems. Aiming to be able to construct a proper model of the microscope within the next few days.</div>'));

graph.commit('design', 'Hardware Design', $('<div>21 July 2015: Second prototype is on the magnetic board: with proper holders and alignment. Viewed some plant cells under bright field - including the alga Spirogyra, where we could see the chloroplasts forming a triple helix pattern. Quality check - done! Hardware team now aspire to engineer a system for automated movement on the magnetic board. Focusing is quite tricky for now. Also received a real optical bench from the Cavendish Lab (Department of Physics). Just for comparison. Ours is better of course...</div> <div class="teamen"><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/4/46/CamJIC-Notebook-Spirogyra.jpeg)"><div class="blur"></div><div class="profile"><h3>Imaging</h3><p>Spirogyra (algae) cells imaged with our prototype of a microscope under brightfield. The helical arrangement consists of their chloroplasts.</div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/9/90/CamJIC-Notebook-Prototype2.jpg)"><div class="blur"></div><div class="profile"><h3>Hardware & Optics</h3><p>Second prototype assembled on magnetic board with 3D printed plastic holders and some magnets. No more cardboard! Perfect for teaching purposes.</div></div></div>'));

graph.commit('optics', 'Optics', $('<div>21 July 2015: Figured out that when capturing an image with the Raspberry Pi Cam, a red LED on the board flashes and this somehow colours our pictures in green. Will have to deactivate it. Simplest solution: just cover with some black paint.</div>'));

graph.commit('optics', 'Optics', $('<div>22 July 2015: Update on the LED problem - a simple How To Fix: <ol> <li>Open Terminal, type in: sudo nano /boot/config.txt and hit enter.</li><li>Go to the bottom of the file and type in disable_camera_led=1, then press Ctrl+X, hit Y and press Enter.</li><li>Done! </li></ol> Dichroic filters arrived today. We will be in fluorescence mode soon! Still working on the hardware side of the setup, though.</div>'));

graph.commit('design', 'Hardware Design', $('<div>23 July 2015: Some advice on 3D printing - when designing holes/holders make them slightly bigger than your actual thing. Because the printer always makes them too small. We found this out the difficult way! More 3D printing advice coming soon: including a guide on how to choose the correct temperature for the particular part being printed.</div>'));

graph.commit('sw', 'Software', $('<div>24 July 2015: Working on a Google Maps-like interface for our screening system. Coming soon! Never before has live observation of your samples from away been so smooth. Already being tested on a picture of <i>Marchantia</i>. Will be available in desktop/mobile versions.</div>'));

graph.commit('optics', 'Optics', $('<div>24 July 2015: Assessment of our bright-field microscope prototype: field of view width 0.2mm, resolution - well under 10 microns. Also assessed different filters (cheap vs. more expensive options). A review of these coming next week, along with fluorescence microscopy setup. Finally managed to print and assemble the fluorescent cube today. As an aside, accidentally discovered how important illumination of the sample is, because the torch we were using went battery low, and made it pretty much impossible to focus on any image.</div>'));

graph.commit('sw', 'Software', $('<div>25 July 2015: Tweaked our wiki design\'s menu bar. Previously, if you moved the mouse off the submenus while trying to reach a link, the submenu would disappear to much frustration. Now it will allow a grace period before fading out, allowing your mouse to recover onto the menu! Try it out!</div>'));

graph.commit('optics', 'Optics', $('<div>27 July 2015: Comparison of our prototype with a lab bench microscope Nikon Labophot (retail price around 1,500$). See photos of Pinus stem crossection below. Quality achieved is totally comparable, magnification 400x. We still have some issues with colour, probably due to the illumination by UV LED torch. Resolved temporarily by putting in a yellow filter. Also, first attempts on fluorescence today. Failed. More tomorrow.. </div> <div class="teamen"><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/0/02/CamJIC-Notebook-PinusStem.jpg)"><div class="blur"></div><div class="profile"><h3>Our Image</h3><p>Achieved coloured image.</div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/f/fa/CamJIC-Notebook_PinusStemNikon.JPG)"><div class="blur"></div><div class="profile"><h3>Nikon Image</h3><p>Image obtained with Nikon microscope and digital camera mount. Compare the quality yourself (and the price).</div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/8/8b/CamJIC-Notebook-Lab.jpg)"><div class="blur"></div><div class="profile"><h3>Wet Lab</h3><p>A biologist and an engineer in the wet lab. Sounds like the start of a joke, but they are actually preparing Marchantia for observation under our to-be-constructed fluorescent microscope. Fully dressed, according to all safety regulations.</div></div></div>'));

graph.commit('march', 'Marchantia', $('<div>27 July 2015: Prepared some microscopic slides with fluorescent <i>Marchantia</i> transformants (express GFP), generously provided by the Haseloff Lab. However, able to look at them only through the lab fluorescence microscope for now. In the meantime, enjoy this simple <i>Marchantia</i> sample prep protocol: <ol> <li>Use No. 8 cork borer to cut cylinders of carrot core approx. 50 mm long.</li> <li>Place in 70% ethanol and leave overnight (will lose colour).</li> <li>Cut cylinders in half longitudinally, and place sample between halves (thin sample e.g. <i>Marchantia</i> leaf).</li> <li>Put halves back together with sample at one end, sandwiched in place.</li> <li>Insert the cylinder of carrot into a hand-held microtome.</li> <li>Cut thin slices of carrot + sample using microtome knife.</li> <li>Wash thin sections into beaker using deionised water.</li> <li>Use a pasteur pipette to pick up sample in a drop of water, and drop onto a slide (note: do not include carrot tissue).</li> <li>Cover with glass slip and visualise (brightfield or fluorescence).</li></ol></div>'));

graph.commit('optics', 'Optics', $('<div>28 July 2015: Final tinkering with the optics for bright field microscopy. Done! We managed to achieve a full-colour image by simply changing our illumination to a bright white LED. Done with this now! Getting ready for fluorescence: printing a redesigned cube with our new 3D printer.</div>'));

graph.commit('design', 'Hardware Design', $('<div>28 July 2015: Now that we have a new (and large enough) 3D printer - the Ultimaker 2, we will finally be able to print our chassis in full size. Still polishing off the SCAD designs. Will try to print it overnight.</div>'));

graph.commit('sw', 'Software', $('<div>28 July 2015: We went crazy, pulled a late night yesterday and also spent this morning making our wiki design mostly fully responsive. Now we have one template to rule them all, and full mobile browser support!</div>'));