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

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graph.commit('design', '3 August 2015', $('<div><h4>Hardware Design</h4>We managed to get our hands on an inexpensive Shapeoko v.1 (this is a motorised x,y-positioning stage). We will try and adapt it for our microscope to be mounted on. Hello easy scanning of large samples of cells/colonies!</div>'));
 
graph.commit('design', '3 August 2015', $('<div><h4>Hardware Design</h4>We managed to get our hands on an inexpensive Shapeoko v.1 (this is a motorised x,y-positioning stage). We will try and adapt it for our microscope to be mounted on. Hello easy scanning of large samples of cells/colonies!</div>'));
 
graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4> We went on a bug-fixing spree, and as usual the 80:20 rule applied with the last class taking most of the day to fix :( Now we have a fully functional virtual XY stage to play with until the Shapeoko is setup! For now we can explore the skies with a gigapixel image of Andromeda.</div>'));
 
graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4> We went on a bug-fixing spree, and as usual the 80:20 rule applied with the last class taking most of the day to fix :( Now we have a fully functional virtual XY stage to play with until the Shapeoko is setup! For now we can explore the skies with a gigapixel image of Andromeda.</div>'));
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graph.commit('sw', '5 August 2015', $('<div><h4>Software</h4> The Shapeoko\'s now fully setup with a nice python CLI interface controlling it from the comfort of our laptops.</div>'));
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graph.commit('sw', '5 August 2015', $('<div><h4>Software</h4> The Shapeoko\'s now fully setup with a nice python CLI interface to control it from the comfort of our laptops.</div>'));
 
graph.commit('optics', '6 August 2015', $('<div><h4>Optics</h4>First signs of fluorescence detected! Finally.</div>'));
 
graph.commit('optics', '6 August 2015', $('<div><h4>Optics</h4>First signs of fluorescence detected! Finally.</div>'));
 
graph.commit('design', '', $('<div style="margin-top:-40px"><h4>Hardware Design</h4>Printing our third attempt on the microscope stage currently. Already managed to adapt the z-axial movement with a screw for precise focusing. In the meantime, playing around with our Shapeoko.</div>'));
 
graph.commit('design', '', $('<div style="margin-top:-40px"><h4>Hardware Design</h4>Printing our third attempt on the microscope stage currently. Already managed to adapt the z-axial movement with a screw for precise focusing. In the meantime, playing around with our Shapeoko.</div>'));
 
graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4> Challenge time &mdash; We acquired a 100-frame GIF containing over six hundred moving pixels and raced to build our own specimen-tracking algorithms! We got some very nice entries and even managed to extrapolate their movement back in time.</div>'));
 
graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4> Challenge time &mdash; We acquired a 100-frame GIF containing over six hundred moving pixels and raced to build our own specimen-tracking algorithms! We got some very nice entries and even managed to extrapolate their movement back in time.</div>'));
 
graph.commit('design', '7 August 2015', $('<div><h4>Hardware Design</h4>Microscope stage fully set up, with manual moving of the sample and focusing, but quite impressive precision, focusing and stability. Unfortunately cannot show any of our designs yet due to intellectual property and licensing issues. By the way, more on this topic coming soon on our Human Practices page.</div>'));
 
graph.commit('design', '7 August 2015', $('<div><h4>Hardware Design</h4>Microscope stage fully set up, with manual moving of the sample and focusing, but quite impressive precision, focusing and stability. Unfortunately cannot show any of our designs yet due to intellectual property and licensing issues. By the way, more on this topic coming soon on our Human Practices page.</div>'));
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graph.commit('design', '10 August 2015', $('<div><h4>Hardware Design</h4>Tested maximum movement of our 3D printed stage. Details to be released shortly. We also analysed the bending of the z-axis support under different loads. The Shapeoko  z-axis limit-switch needed tinkering with, as it was too wobbly. This was solved with a couple of rubber bands. Classy.</div>'));
 
graph.commit('design', '10 August 2015', $('<div><h4>Hardware Design</h4>Tested maximum movement of our 3D printed stage. Details to be released shortly. We also analysed the bending of the z-axis support under different loads. The Shapeoko  z-axis limit-switch needed tinkering with, as it was too wobbly. This was solved with a couple of rubber bands. Classy.</div>'));
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graph.commit('design', '11 August 2015', $('<div><h4>Hardware Design</h4>Overnight we ran a time-lapse using our microscope, taking images of a micrometer scale every 5 minutes. We then used a free, open-source video tracking software called <a href="http://physlets.org/tracker" class="blue">Physlets Tracker</a> which enabled us to analyse the long-term drift of our microscope stage by tracking a single point over the time-lapse.</div>'));
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graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4> We rewrote our Shapeoko interface to handle hotplugging, waiting on command completion, and continuous position updates.</div>'));
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graph.commit('design', '11 August 2015', $('<div><h4>Hardware Design</h4>Overnight we ran a time-lapse using our microscope, taking images of a micrometer scale every 5 minutes. We then used a free, open-source video tracking software called <a href="http://physlets.org/tracker" class="blue">Physlets Tracker</a> which enabled us to analyse the long-term drift of our microscope stage by tracking a single point over the time-lapse.<br>Also, working towards automated stage movement. Wired up an Adafruit unipolar stepper motor to an Arduino, which turned out not to be so straightforward. The motor successfully rotates a bolt to screw it into a nut... but might be not powerful enough for operating the microscope. If only I could take the motors from the Shapeoko or the Ultimaker...</div>'));
 
graph.commit('design', '12 August 2015', $('<div><h4>Hardware Design</h4>The morning was spent in the Department of Engineering, doing 3-point bending tests on 3D printed material using the Instron machine. We were analysing different thicknesses of samples and different printing styles and comparing strength and flexibility. Ultimately this will allow us to see which parts of our microscope are more likely to fail.</div>'));
 
graph.commit('design', '12 August 2015', $('<div><h4>Hardware Design</h4>The morning was spent in the Department of Engineering, doing 3-point bending tests on 3D printed material using the Instron machine. We were analysing different thicknesses of samples and different printing styles and comparing strength and flexibility. Ultimately this will allow us to see which parts of our microscope are more likely to fail.</div>'));
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graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4> Our Shapeoko interface is now fully integrated with the rest of our software library! We can now use smart action queueing, and automated image scanning is coming soon (when we mount the microscope on it) &mdash; stay tuned for an awesome new microscope interface!</div>'));
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graph.commit('optics','13 August 2015',$('<div><h4>Optics</h4>Swapped the cheap (and not really sufficient) filters for Comar dichroics. Had to do some super safe glass cutting to make them fit. With this optical set up inside the fluorescence cube, finally managed to register fluorescence properly! Having some issues with the Raspberry Pi camera, though: it tries to be too smart and calculate white balance and exposure time... which actually makes our images worse. Sigh... Working on it.</div>'));
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graph.commit('optics','17 August 2015',$('<div><h4>Optics</h4>FLUORESCENCE IS WORKING. We changed the lighting from the LEDs we were using earlier to an arc lamp we lifted off of the department. Boom, GFP beads have been imaged. Now we just need to make it work with our lights and for other wavelengths.</div>'));
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graph.commit('design','26 August 2015',$('<div><h4>Hardware Design</h4>This week and a half has been a busy one on the hardware front. We have redesigned our epicube to be much more compact whilst reducing the leaking of light resulting in higher quality images: almost comparable to the Lab microscope! The motors have been powered up so we can get our x-y-z movement automated and the chassis has undergone some minor tweaks and improvements.</div>'));
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graph.commit('optics', '', $('<div style="margin-top:-40px"><h4>Optics</h4>We have “Resolved” a few problems this week! Brighter LEDs have arrived (for both GFP and RFP) and some new filters for RFP have come in.  Using a sapphire ball lens has helped to improve our resolution substantially and some calculations and testing has been done to select the correct filters for fluorescence and optimise the microscopes field of view and resolution – requests for new designs to be sent to the Hardware folk!</div>'));
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graph.commit('design','27 August 2015',$('<div><h4>Hardware Design</h4>We visited the John Innes Centre in Norwich today and met the NRP-UEA iGEM team. We learned all about their project and gave a presentation about ours! We were also planning to give a demonstration of our hardware, but unfortunately due to technical issues we weren\’t able to set up our microscope properly. Lesson learnt: make the microscope easier to assemble on the go and more reliable. .</div>'));
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graph.commit('design','28 August 2015',$('<div><h4>Hardware Design</h4>We\’ve received a proposal for a new translation stage design – not sure whether to take it. The project is heating up and we set up a division of labour for the coming week. Ordered RFP imaging equipment and we should hopefully have a fully working prototype by the end of the week! .</div>'));
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graph.commit('meta','4 September 2015', $('<div><h4>Collaboration</h4>Went down to London for the UK iGEM teams meet up organised by the University of Westminster. Had some great time there, presenting our project and showing off with our flawless microscope at an exclusive workshop.</div>'));
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graph.commit('sw','8 September 2015', $('<div><h4>Software</h4>After a long night, the motorised control has been perfected! :) Power saving mode, smooth acceleration and deceleration, asynchronous movement of different axes at the same time, as well as control over it using the arrow keys in webshell has all been implemented and wired up now.</div>'));
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graph.commit('design','9 September 2015', $('<div><h4>Hardware Design</h4>Our microscope design has been finalized. Looks flawless! Sadly, no more OpenSCAD tinkering. Now we can concentrate on documentation of our project work.</div>'));
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graph.commit('sw','', $('<div style="margin-top:-40px"><h4>Software</h4>Image stitching works! At long last, micromaps has a shot at working! We are able to even remove artefacts of dust on the sensor by overlaying several images. Combined with motor control, which allows for really fine control over the axes, things are looking positive!</div><div class="teamen"><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/d/d9/CamJIC-Notebook-StitchCode.jpg)"><div class="blur"></div><div class="profile"><h3>The code responsible</h3><p>It includes general 2D stitching, though is a bit memory inefficient and can\'t tell if an image doesn\'t stitch well!</p></div></div><div class="face facen" style="background-image: url(//2015.igem.org/wiki/images/0/00/CamJIC-Notebook-StitchSuccess.png)"><div class="blur"></div><div class="profile"><h3>Success!</h3><p>At long last, with much gratitude to the perfection of our motorised stage so that we could get the underlying high quality images.</p></div></div></div>'));
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graph.commit('optics', '14 September 2015: 4 days to Wiki Freeze', $('<div><h4>Optics</h4>Last minute changes to the microscope. Have just incorporated a module for darkfield imaging into the stage. Improvements to fluorescence epicube: realized these are really necessary after some serious struggle with imaging the samples we receiver from the teams we collaborate with.</div>'));
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graph.commit('design', '', $('<div style="margin-top:-40px"><h4>Hardware Design</h4>Doing some filming these days. Starring: OpenScope. Make Your Own video coming soon.</div>'));
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graph.commit('meta', '15 September 2015: 3 days to Wiki Freeze', $('<div><h4>Wiki</h4>Everybody working hard on finishing up the project and Wiki content. Also, enjoying some creative design work in the meantime (check out our new Home page). All-nighter sessions in the lab.</div>'));
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graph.commit('sw', '', $('<div style="margin-top:-40px"><h4>Software</h4>After an 8am-8am all-nighter, the MicroMaps graphical interface, and much of the behind-the-scenes logic, is complete! Unfortunately, technical issues with image stitching reliability have forced us to remove key features, leaving MicroMaps in early alpha stage for the time being.</div>'));
  
 
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Latest revision as of 16:44, 18 September 2015

CAMBRIDGE-JIC

Notebook