popSCOPE: Pop bottle digital microscope to run your own biological experiments

prusaprinters

3D files included here at Prusa Printers: <ol> <li>All parts to make your own popSCOPE.</li> <li>26x 3D printable QR-code microscope slides which are used to simulate real microscope slides</li> <li>18x puzzle piece files (glued together to form 9 puzzle pieces in the end. These are used in the DNAscope activity.</li> <li>Test tube holders - Included multiple files for different width test tubes. I recommend measuring the width of your tubes and using the holder with the closest dimension since a tight fit ensures the tube stands straight.</li> </ol> Activities included with popSCOPE: <ol> <li><a href="https://scopeseducation.org/tutorials/displayscope/" target="_blank">DisplaySCOPE</a>: View digitized samples from real labs.</li> <li><a href="https://scopeseducation.org/tutorials/chronobioscope/" target="_blank">ChronobioSCOPE</a>: Run your own real biological experiments.</li> <li><a href="https://scopeseducation.org/tutorials/dnascope/" target="_blank">DNAscope</a>: Learn about DNA and environmental DNA (eDNA). </li> </ol> Complete assembly instructions, including basic lesson plans and explanations of all included files, can be found <a href="http://scopeseducation.org/wp-content/uploads/popSCOPE%20documentation.pdf" target="_blank">here.</a> More information about SCOPES Education: <a href="https://scopeseducation.org/">https://scopeseducation.org/</a> Video tutorials for all activities can be found at: <a href="https://scopeseducation.org/setup/">https://scopeseducation.org/setup/</a> Download for Raspberry Pi disk image: <a href="https://scopeseducation.org/downloads/">https://scopeseducation.org/downloads/</a> What is SCOPES? SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science) is an open-source STEM didactic tool that is self-contained, independent of local resources and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. Our design philosophy: We have developed SCOPES as a cost-effective platform to bring life science labs to the classroom. SCOPES is designed to be a modular platform that can be easily adapted for the specific needs of the educator, even without any computer or programming skills. During the design of SCOPES, we considered resource limitations that some classrooms might face. While dedicated computer classrooms in schools are becoming standard in developed countries, buying new hardware is both time consuming and expensive. Sometimes a stable source of electricity might also not be available in some areas. Therefore, we chose the Raspberry Pi Zero W (Pi for short) which is a tiny, power-efficient computer, to be the brains of our project. The Pi is powered via a 5V USB port that is commonly used for charging smartphones and tablets and can be run remotely from a battery or small solar panel. We also do not want you to have to run out and buy a new screen or adapter. Therefore, we chose to make use of your mobile devices to display the visual output of SCOPES. The Pi acts as a wireless access point that mobile devices can connect to and display information provided by the Pi. Several devices can connect to SCOPES in parallel, allowing for multiple young scientists to interact with an individual SCOPES. Thus, SCOPES is self-contained and can be operated in the complete absence of any infrastructure with just a mobile device and a battery. Why are we using a pop bottle and not 3D printing the entire case? This is a great question and it comes back to our design philosophy. We purposely want to keep costs to a minimum, and for some, that might mean they have limited access to a 3D-printer. Therefore, we tried to minimize both the amount of material required to print and the number of additional parts required to build and assemble the popSCOPE case. There is also the environmental aspect and we felt that including “found” material and encouraging recycling, is an important lesson in itself. Also, some materials can be substituted for other components if necessary. For example, in most cases, M3 screws can be substituted with zip ties or similar thin material. Custom User Interface: We have developed a custom web-based interface that makes operating SCOPES simple and doesn’t require any prior programming knowledge. As SCOPES builds on open-source Raspberry Pi hardware, it can be readily adapted for novel projects. We also anticipate that through collaborative learning, SCOPES will encourage interdisciplinary experiential learning where programming skills are used to explore biological concepts and thus bridge several STEM disciplines. An example might be that students build the popSCOPE case, follow tutorials on how to program time-lapses on the Raspberry Pi, and then use this to perform a biological experiment as described for the ChronobioSCOPE (see above). In this way, SCOPES facilitates hands-on interdisciplinary learning and problem-solving opportunities for students. SCOPES can also be expanded using the exquisite capabilities of the Raspberry Pi to interact with a spectrum of sensors to record environmental parameters. SCOPES 2.0 The popSCOPE case is an updated version of our original SCOPEScase. The original version can be made from laser-cut plywood, and if you are interested in learning more about this, we recommend visiting our website to find all the files (<a href="http://scopeseducation.org">http://scopeseducation.org</a>). Our goal in making the popSCOPE 3D printable was to hopefully make this project available to a wider audience. Parts required (See figure) 3D printed parts: <ol> <li>1x PiMount</li> <li>1x Left arm bracket (provided varying lengths, depends on the bottle)</li> <li>1x Right arm bracket (provided varying lengths, depends on the bottle)</li> <li>1x Camera/LED mounting bracket</li> <li>1x Lid</li> <li>1x Stabilizer base</li> </ol> Electronic parts: <ol> <li><a href="https://thepihut.com/products/raspberry-pi-zero-w?variant=547421782033" target="_blank">Raspberry Pi Zero W</a> (simpler if the male header is already attached to the GPIO pins)</li> <li><a href="https://thepihut.com/products/raspberry-pi-camera-module" target="_blank">Raspberry Pi Camera v1 or v2</a></li> <li><a href="https://shop.pimoroni.com/products/blinkt" target="_blank">Pimoroni Blinkt LED</a></li> <li><a href="https://thepihut.com/products/noobs-preinstalled-sd-card" target="_blank">Micro SD Card</a></li> <li><a href="https://thepihut.com/products/adafruit-premium-female-male-extension-jumper-wires-40-x-12-300mm" target="_blank">Male to female jumper cables (30 cm)</a></li> <li><a href="https://thepihut.com/products/raspberry-pi-zero-camera-cable-300mm" target="_blank">Pi Zero camera cable (30cm)</a></li> <li><a href="https://thepihut.com/products/beaglebone-universal-power-supply-5v-2a" target="_blank">5V power adapter/power supply</a></li> </ol> Additional parts: <ol> <li>M3 Screws and nuts (8x 10 mm, 2x 14 mm or longer)</li> <li>Screwdriver</li> <li>Empty 1.5 L or 2 L coke bottle</li> </ol> Note: The screws can be substituted for zip ties if needed. Coke bottle may be substituted for any other bottles where the cap threads are the same and the bottle is wide enough. FAQ: Why not just make a mobile app that does everything SCOPES can do? We get this question regularly and understand that the above activities might seem simpler to do as an app. While we agree the popSCOPE case may not be essential, however, we are convinced it provides improved didactic user experience and increases the consistency of experiments. We believe that there is also value in including didactic concepts in the classroom and that not all learning should be purely app-based. A recent report from the OECD agrees with this notion and states that while many developed nations have been quick to adopt digital communication platforms in the classroom, without dedicated didactic concepts these methods can have a negative influence on learning outcomes (OECD, 2015. Students, Computers and Learning). The act of building something with a student, instead a store-bought solution teaches them the value of engineering and problem-solving. We wanted to make this an open-source system that could be modified and tinkered with by other users, who probably have even better ideas than us! By incorporating Raspberry Pi hardware, we can also introduce a host of other sensors to create far more complicated measurements and experiments. And most importantly, do you really want to be without your mobile phone for a week while you film a plant timelapse? ;) What else can I do with my SCOPES? Currently, SCOPES comes preloaded with three activities. The DisplaySCOPE, the ChronobioSCOPE, and the DNAscope. We are striving to create additional fun and educational activities and recommend that you check back on our website regularly for updates. If you have any great ideas for projects or suggestions for future improvements, please leave us a note in the comments section! Thank you for checking out popSCOPE! If you like this project please leave a comment or review, and share us with your friends. This is an entry for the Prusa Design "Educational Items" contest. If we win, we plan to use this printer to mass-produce and share popSCOPE with school children everywhere. Assembling the popSCOPE <ol> <li>Download and install the <a href="https://scopeseducation.org/downloads/" target="_blank">FlaskSCOPE disk image</a> on the SD card. This can be found on our website or our <a href="https://github.com/scopeseducation/flaskSCOPE" target="_blank">github page</a>. We provide some advice with installation on our github page, but since the process of installing raspberry pi disk images on an SD card can vary depending on the operating system you are using, we suggest the reader follows the <a href="https://www.raspberrypi.org/downloads/raspbian/" target="_blank">well-prepared guides</a> by the Raspberry Pi Foundation for more information. </li> <li>Insert the SD card into the Raspberry Pi Zero W (now referred to simply as Pi). </li> <li>Secure the Pi to the 3D printed piMount with 4 screws. You will see a little grove in the piMount, which should provide space for the header on the GPIO pins. </li> <li>Screw the piMount onto the bottle. Mark where the two small wings stick out on the bottle by drawing two little lines on the bottle. Remove the piMount from the bottle. </li> <li>Hold the piMount with the two arm brackets in place, directly above the bottle opening (see photo) so that the arm brackets are touching the bottle. Make sure that the arms are lined up with the two small marks you made in the previous step! They should also be held perpendicular to the piMount. Now draw two more small marks where the arms both make contact with the bottle. Note: Included are a variety of lengths for this piece since the bottle you are using may vary than the standard Coke bottle here in Austria. For a 1.5 L coke bottle which I sourced locally, it seems the 8cm arms work well, but this may vary region to region. My suggestion would be to measure the width of the bottle to determine how far the mount needs to extend. The bottle needs to be at least 8cm wide to hold the camera/LED mount comfortably. </li> <li>Draw a large rectangle on the bottle as shown in the photo. This will serve as a guide for cutting in the next step. </li> <li>Cut out this rectangle. This step and the next should be performed by an adult. </li> <li>Using the marks from step 5, cut two small holes in the bottle to let the arm brackets pass through. </li> <li>If there is any liquid remaining in the bottle, now is a good time to wipe it out. </li> <li>Screw the piMount back onto the bottle. Slide the arm brackets in place, so that they extend into the bottle. Hold both arms along with the L-shaped stabilizer arms in place with 2x 16 mm M3 screws (minimum length of screws is 12 mm) as shown in the photo. </li> <li>Preparing the camera and LED mounting bracket. Place the LED strip in the mounting bracket, paying careful attention to the curve on one side of the LED. This should be pointed away from the camera. </li> <li>Place the camera in the camera mounting bracket so that the cable mount is pointed away from the 8 little holes. The version of Raspberry Pi camera does not matter at this point (v1 or v2 work equally well). </li> <li>Place the lid over the camera and LED strip. </li> <li>Secure the camera and LED strip in place by using the lid piece. Use 2x 10 mm M3 screws. </li> <li>Run the camera cable and the jumper cables up through the bottle and out the hole in the piMount. Run the camera cable through the small grove on the bottom of the piMount and loop it over before plugging it into the Pi. Be very careful to not bend or twist this cable, it is very fragile. </li> <li>Plug the 4 jumper cables into the 4 pins listed in the diagram below. Make note of which cable is plugged into which pin since we will need to use the same pin order for the Blinkt LED. Image <a href="https://pinout.xyz/pinout/blinkt#" target="_blank">from.</a> </li> <li>The wiring should look something similar to this: </li> <li>Now plug in 4x jumper cables into the LED strip according to the pinout diagram in step 16. Be careful to plug in your Blinkt the correct way round, it has curves on the top that match the corners of your Raspberry Pi. For more information regarding the details of this LED strip please see <a href="https://shop.pimoroni.com/products/blinkt" target="_blank">Pimoroni</a>. The order of the cables should be exactly the same as the way you plugged them into the GPIO (see pinout diagram above). Plug in the camera cable into your camera. Be careful since the cable is very delicate. Make sure the orientation is correct when inserting. </li> <li>Now attach the camera and LED mounting bracket to the arm brackets extending from the piMount. This requires 2x 10 mm M3 screws and nuts. The nuts can be placed into the holes in the arms. </li> <li>Your popSCOPE is now complete! Plug it into a 5V power adapter and power it on! </li> <li>If you wish to use the ChronobioSCOPE horizontally for time-lapse experiments, we recommend attaching the adjustable stabilizer base to the L-shaped stabilizer arms. This prevents the bottle from rolling over. </li> <li>For information regarding connecting mobile devices to your popSCOPE or using the <a href="https://scopeseducation.org/tutorials/flaskscope/" target="_blank">FlaskSCOPE</a> interface, please visit our website for more <a href="https://scopeseducation.org/setup/" target="_blank">tutorials</a>. </li> </ol>

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