Difference between revisions of "Team:Cambridge-JIC/Notebook"
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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="team"><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('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="team"><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="team"><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 | + | 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="team"><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 | + | 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>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="team"><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('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="team"><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>')); | ||
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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('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('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 | + | 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('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>')); | ||
Revision as of 14:11, 28 July 2015
