Update in progress
More updates coming up, including a description of my final projects (early-stage experiments on predefined microbes/substances detection with a spectrophotometer and a microscope using computer vision - related libraries) and an instructable on... the laser cutter :-)
Chromatography
Black and blue ink separation with Whatman paper.
3D printing
So far I tried to print the barrel for the microscope (and it went fine) and the rotor for the centrifuge: apart from the fact that for the centrifuge I could only find a different motor from the one suggested in the bill of material, before 3D printing the whole part I was also instructed to perform some preliminary tests of the part of the rotor critical for this design: the central hole in which the motor shaft should tightly fit in. The yellow rotor is nice to see, but it does not work as the hole for the shaft is a bit too big for the motor...
Prototypes preview /2
The electronics on the incubator up and running... The only problem I encountered is to find/create a larger box to fit it in on the top of the incubator itself.
Laser cutter/2
My relationship with the laser cutter has been not so simple so far. From the beginning of the Academy unexpected problems have occurred, such as weird behavior opening SVG files created in Inkscape (the version included in my Linux computer, running Lubuntu 14.04) and the Adobe Illustrator CS5 present on the Windows computer of the Fab Lab hooked up to the Laser Cutter: the files would never been of the right dimensions and the relatively simple solution was to open the SVG files in the Windows version of Inkscape and from there copy and paste them into Illustrator.
Another issue I encountered with the machine was the importance of a proper manual focus, especially if you want to be able to laser cut a bit faster: in the first cuts I used a speed of 0,7-0,8, then we tried to increase up to 1.1 to return to 0.9 because it would not work satisfactorily: at 0.9 after focusing carefully it would be still difficult sometimes to detach the laser cut pieces from the rest of the wood. The material I used was almost always 3mm MDF.
Sometimes it would also work correctly :-)
Notes on photobacterium phosphoreum /2
Unfortunately so far Giacomo and I failed to have these photobacteria shine, both following the DIY growth medium protocol and the "traditional lab" one: we also tried to oxygenize the cultures with an acquarium pump, having it running in the flasks from 15, 30 or 45 minutes.
Notes on photobacterium phosphoreum
source: http://mic.sgmjournals.org/content/72/2/415.full.pdf
yeast extract, aeration, pH and temperature produced the most dramatic effects
per litre of deionized water: yeast extract (Fisher Scientific), 5 g; tryptone (Fisher Scientific), 5 g; NaCI, 30 g; Na2HPO4,, 5 g; KH2PO4, I g; glycerol, 3 ml.
The liquid cultures were grown in Erlenmeyer flasks with cotton plugs with the volume of sterile medium 115 the volume of the flask. The cultures were incubated at 15 "C, unless specified otherwise, with vigorous shaking.
Bacteria for extraction of luciferase were harvested by centrifuging in an RC-2B Sorvall centrifuge with a GSArotor at 10 ooorev/min for I 5 min. For the light measurements in vitro the organisms were lysed in deionized water and the debris removed by centrifuging as described above.
Growth at both pH 6.0 and 6.5 gave maximum luminescence rates per bacterium. The growth rate and yield was about 50 % higher at pH 6-5 than at pH 6.0. Therefore, the bacterium was cultured in the standard medium at pH 6.5.
Bacterial bioluminescence is absolutely dependent upon oxygen. Vigorous shaking of cultures grown in flasks as described in Methods was adequate to produce maximum luminescence rate per bacterium without additional aerating apparatus.
3D Lab tool in Sketchup
Laser cutter
Interesting tutorial for getting started: the three-part video by the Stanford University Transformative Learning Technologies Lab. http://tltl.stanford.edu, and the FabLab@School Project
https://www.youtube.com/watch?v=BXtWkFR1Oys
Preview of the prototypes
Screen pixels test video with webcam microscope
The microscope/2
I was stimulated by some part of the lecture about the calculation of the magnification obtainable by the webcam microscope, and I tried to establish how much mine was magnifying.
With relation to the 640x480 image i was seeing on my scren, which measured at 100% size 16x12cm with about 3 observable pixels in it, I tried to calculate the actual size of a pixel on my screen:
my display has a native resolution of 1366X768 (10.11" × 5.68" = 57.48in² (25.68cm × 14.44cm = 370.86cm²) at 135.09 PPI, 0.188mm dot pitch, 18250 PPI² ) which makes a single pixel about 1/18250 I².
The image of a single pixel I have obtained is about 64cm², that is 9.92 square inches
So the magnification on the screen should be: 9.92 / (1/18250)= 181.040 times!
But this is not the actual magnification of the microscope, as I think that should be calculated against the area of the webcam image sensor:
http://www.siliconimaging.com/Lens%20Image%20formats.htm http://en.wikipedia.org/wiki/Image_sensor_format#Table_of_sensor_formats_and_sizes
Considering an image sensor of about 1/4" (or less), we can calculate the area of the sensor as about 7.68 square mm, that is 0.076 square cm (0.0119 square inches), and obtain a final calculation of (0.0119/3)/(1/18250) = approximately 72.391 times with a 1/4" sensor, but up to 7 times less in case of smaller image sensors.
Other resources:
http://web2.0calc.com/ http://www.instructables.com/id/DIY-Microscope/?ALLSTEPS
http://hackteria.org/wiki/index.php/Laser-cut_microscopy_stages in particolare il kit con il microscopio con il servo motor ed arduino
http://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion/?ALLSTEPS
The microscope
In order to get the four needed lenses, I tried to take apart some single-use cameras from kruidvat as suggested. Reading about the potential dangers of the high voltage circuit with charged capacitor connected to the flash unit, I tried to get some rubber/insulated gloves like the ones electricians use, but no one I asked had anything similar at the fablab. Then I tried with a spatula with a wooden handle and although working very cautiously the camera emitted a spark near the battery compartment (battery had already been removed), also relatively away from the flash unit.
At the moment, I am still alive... :-)
Other interesting resources about DIY microscopy:
Cellphone microscopy https://www.youtube.com/watch?v=VH5H6uSQUFE
Making a LEGO microscope: http://www.microbehunter.com/making-a-lego-microscope/
Make webcams work in Linux https://help.ubuntu.com/community/Webcam
The incubator
I ran into some problems with the multidigit 7-segment display: I bought the one from EOO (LTC-5837WC) http://www.eoo-bv.nl/index.php?_a=viewProd&productId=8390, but it seems differently wired compared to the other one https://iprototype.nl/docs/led-bar-4xsegment-red-technisch-datasheet.pdf.
Before buying it I did not notice that it has 40 pins, the other 16 : according to the datasheet of the former, (http://datasheet.octopart.com/LTC-5837WC-Lite-On-datasheet-13708537.pdf) the difference seems to be that the "corresponding" segments of each digit are not linked together, which makes difficult to control the display with an arduino uno as more pins than the total amount available on the board would be needed (it seems to be not "multiplexing-ready").
I had to manually link each of the corresponding segments to each other on the breadboard in order to get it to work.
Here is a picture of the mess, just to give an idea of the situation on the breadboard... ;-):
Building and managing a documentation site on GitHub
I found this method to upload images etc to github without using git/the command line relatively useful to build simple pages with the automatic generator: http://solutionoptimist.com/2013/12/28/awesome-github-tricks/