Contents

Introduction ............................................................................................................................................. 1

Preparing the 3D Printed popSCOPE Case ............................................................................................. 2

DisplaySCOPE ...................................................................................................................................... 12

ChronobioSCOPE ................................................................................................................................. 12

DNAscope Introduction ........................................................................................................................ 13

DNAscope Activity: .............................................................................................................................. 15

Follow-Up Activity Idea: LEGO DNA Sequencing ............................................................................. 16

Follow-Up Activity Idea: Isolating DNA from fruit ............................................................................. 17

Frequently Asked Questions ................................................................................................................. 18

Additional Files Included in this PDF ................................................................................................... 19

Acknowledgements ............................................................................................................................... 19

Introduction

Welcome to SCOPES, we are glad you are here! Before we get into the details of how you can use

SCOPES, we thought we would provide a little background on what SCOPES is.

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.

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.

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 popSCOPES case (see below), follow tutorials on how to program time-lapses on the

Raspberry Pi1, and then use this to perform a biological experiment as described for the

ChronobioSCOPE (see below). 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.

We are excited to share SCOPES with you and hope you can use it to explore the world with your young

scientists, helping them to develop critical problem-solving skills.

Below we include a brief overview of what you can do with SCOPES and some guidance on how to

get started. For more information and video tutorials, and all the latest updates, please visit our

website.

Preparing the 3D Printed popSCOPE Case

To begin our journey, we need to build some lab equipment! The most important piece of equipment

for the following experiments will be the popSCOPE case.

The popSCOPE case is a modified 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. We hope that by making the popSCOPE now 3D printable, it

will make this project available to a wider audience.

Parts required (See figure below)

1. 1x PiMount

2. 1x Left arm bracket

3. 1x Right arm bracket

4. 1x Camera/LED mounting bracket

5. 1x Lid

6. 1x Stabilizer base

1 https://projects.raspberrypi.org/en/projects/timelapse-setup

7. Raspberry Pi Zero W (simpler if male header is already attached to the GPIO pins)

8. Raspberry Pi Camera v1 or v2

9. Pimorini Blinkt LED

10. SD Card

11. Male to female jumper cables (30 cm)

12. Pi Zero camera cable (30cm)

13. 5V power adapter/power supply

14. M3 Screws and nuts (8x 10 mm, 2x 14 mm or longer)

15. Screwdriver

16. Empty 1.5 L or 2 L coke bottle

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 bottle is wide enough.

Assembly

1. Download and install the FlaskSCOPE disk image on the SD card. This can be found on our

website or our github page. 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 well prepared guides by

the Raspberry Pi Foundation for more information.

2. Insert the SD card into the Raspberry Pi Zero W (now referred to simply as Pi).

3. 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.

4. 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.

5. 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.

6. Draw a large rectangle on the bottle as shown in the photo. This will serve as a guide for

cutting in the next step.

7. Cut out this rectangle. This step and the next should be performed by an adult.

8. Using the marks from step 5, cut two small holes in the bottle to let the arm brackets pass

through.

9. If there is any liquid remaining in the bottle, now is a good time to wipe it out.

10. 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.

11. 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.

12. 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).

13. Place lid over the camera and LED strip.

14. Secure the camera and LED strip in place by using the lid piece. Use 2x 10 mm M3 screws.

15. 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.

16. 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 from: https://pinout.xyz/pinout/blinkt#

17. The wiring should look something similar to this:

18. 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 Pimorini. 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.

19. 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.

20. Your popSCOPE is now complete! Plug it into a 5V power adapter and power it on!

21. 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.

22. For information regarding connecting mobile devices to your popSCOPE or using the

FlaskSCOPE interface, please visit our website for more tutorials.

DisplaySCOPE

Modern biology is heavily reliant on interpreting visual data obtained through imaging. With

DisplaySCOPE students perform a hypothetical experiment while exploring digitized visual content (in

this case microscope images) by themselves with minimal guidance.

Materials Needed:

1. Assembled popSCOPE case

2. Printed QR-code slides (paper or 3D printed) – Paper slides included below in PDF.

3. Preload digital content

Activity:

Once the individual QR-code slide is placed under the camera, the code is read and the corresponding

microscope image can then be explored by the student. These images can be either sourced from our

website, or a host of other science portals on the web. SCOPES provides an easy-to-use, browser-based

interface to upload digital content (images or movies) and to link these files to one of the provided QR-

codes. SCOPES also allows several students to interact with one SCOPE simultaneously through their

own devices (i.e. tablet, smartphone, computer) and explore the content at their own pace.

ChronobioSCOPE

Many intriguing biological processes are painstakingly slow. For example, plant growth can take

several days before any observable changes occur. Therefore, typical biological experiments in a

classroom are started and then explored at a defined endpoint, which might not capture the interest of

students. To make these experiments more informative, we designed ChronobioSCOPE in a way that

allows students to prepare a time-lapse video of long biological processes.

Materials Needed:

1. Assembled popSCOPE case

2. Idea for a time-lapse experiment

Depending on how you prepare the pop bottle when building your popSCOPE, you can monitor

experiments vertically (i.e. petri dish) or horizontally (ie. plant growth). The progress of the experiment

is monitored by taking consecutive pictures of the transparent reaction chamber or tubes. Finally, all

images can be downloaded and processed on a computer, transforming the lengthy experiment into a

brief movie sequence. SCOPES streamlines the process of filming the time-lapse, monitoring its status

and downloading files. On our webpage, we provide examples of experiments we have performed using

the ChonobioSCOPE.

DNAscope Introduction

DNAscope is an activity that allows young scientists to assemble a sequence of DNA fragments and

identify the species of animal or plant that this DNA came from. In total, 27 different genetic signatures

(animals/plants) are currently supported and this can be adapted and increased if desired. The activity

is performed by having students assemble 3 puzzle pieces into a complete puzzle, representing the gene

sequence of an animal. Each puzzle piece contains a short DNA sequence on one side and a unique QR-

code on the back. When a complete puzzle is placed under the DNAscope it displays the image of an

animal specific to that QR-code combination. The aim of this project is to improve students’

understanding that DNA is the molecule that contains the instructions for life.

Inspired by projects using different colored LEGO bricks to represent the nucleotides in DNA 2,3,

DNAscope provides a new and exciting way for young scientists to learn about DNA. When doing this

activity with your young scientists, begin with the idea that we (Homo sapiens) share 99% of our genetic

information with chimpanzees, one of our nearest evolutionary ancestors. Ask them if we are just like

chimps or if they can name some differences between humans and chimps. If our DNA is so similar,

how could we look so different? Humans and all animals are made up of trillions of tiny little cells. All

the information on how those cells operate is written in their DNA, which can be envisioned as a long

string of four letters repeating in different combinations4. Some parts of this code are similar or

conserved between species and other segments are unique to a single species.

Organisms are constantly interacting with their surroundings and leave behind traces of their DNA

within feces, mucus, hair, leaves, roots or shed skin. Collectively, this is referred to as environmental

DNA (eDNA) and can be purified from water, soil or even air. This lets scientists monitor the different

species living in or transiting through an area even when the animal or plant is long gone.

In this activity, you can perform an eDNA experiment with your young scientists to convey the concept

that a DNA sequence can unambiguously identify a species.

2 https://samnicholls.net/2017/03/15/lego-sequencer/

3 https://www.earlham.ac.uk/articles/earlham-institute-lego-sequencer

4 DNA Structure and Replication: Crash Course Biology: https://www.youtube.com/watch?v=8kK2zwjRV0M

Preparing the 3D Printed Puzzle Pieces

1. There are a total of 9 puzzle pieces. Each puzzle piece consists of two pieces, that are later

glued together. The top half, has a three-letter DNA sequence, and the bottom half has a unique

QR-code. Note: We have also included a paper printable version of these files in this PDF in

case you have limited access to a 3D printer or only want to print the essential parts (ie.

popSCOPE case).

2. Optimally, the pieces should be printed in two colors, so that the raised QR-code and DNA

sequence are a different color than the main puzzle piece. In PrusaSlicer this can be

accomplished by setting the point at which you want to perform a filament change. I would

recommend picking two colors that provide good contrast.

3. To ensure the correct QR-Code is glued together with the correct DNA sequence, there are

recessed numbers on the back of the pieces (A1-A9 and B1-B9). A1 should be glued to B1, A2

to B2, etc. Note: It is not crucial that these are all matched correctly, but it does improve

consistency with the rest of the experiment.

4. Once printing is complete, secure together using super glue or similar plastic bonding agent.

Let dry and the puzzle pieces are now ready for the DNAscope activity!

DNAscope Activity:

1. Prepare PopSCOPE

2. Print (paper or 3D print) the puzzle pieces

3. Hide/bury the puzzle pieces for your young scientists to find/dig up.

4. Have them find 3 pieces that fit together to make 1 complete puzzle. There are currently 27

possible puzzle combinations.

5. On the back of each puzzle piece is a unique DNA sequence. Have your young scientists record

the sequence of the 3 puzzle pieces. This is your secret plant/animals DNA sequence!

6. Next flip the puzzle pieces over and place all pieces in the puzzle tray so that all 3 QR codes

are visible.

7. Make sure the PopSCOPE is in “DNAscope” mode. For more information about how to operate

the PopSCOPE, please visit our online video tutorials. Place the tray with the 3 puzzle pieces

under the PopSCOPE so that it can analyze the “sequence”.

8. On the connected device (ie. mobile phone, tablet, computer), you can now discover which

plant/animal your sequence was from.

9. Repeat experiment again to see which other creatures can be discovered!

Follow-Up Activity Idea: LEGO DNA Sequencing

Now that your little scientist is an expert DNA sequencer, let’s do some more DNA exploration using

LEGO bricks. This is a “bonus” activity and does not necessarily require 3D printing (but the LEGO

compatible bricks can be printed!). All included files can be printed on a standard paper printer and are

attached in this PDF.

Background:

Finally, after introducing the concept of DNA and that different combination of nucleotides can make

different creatures, use the analogy of LEGO bricks so that kids can create their own new neuron. Why

neurons? Well we are neuroscientists and might be a bit biased, but we know these cells are extremely

important for forming neuronal circuits in the brain, and are why we are able to think, write, form

memories and have a unique personality. Furthermore, there is a huge diversity in the number of neurons

that can be produced, and we try to portray the concept that different neurons can have different

functions. These different functions are determined based on which genes are expressed. This

information is all stored in the form of DNA.

Things required:

- Some LEGO bricks (preferably 4 colors, with each color representing a different nucleotide).

If you don’t have any bricks, I highly recommend this great article from Prusa where they

explain how to print a perfect LEGO compatible brick.

- Print DNA sequences/neurons. Make sure to print the files double sided so that on one side is

part of a neuron and the back side is a sequence. Prepare these by cutting them up.

- Print the Neuron Technical Report page so your little scientist can document their experiment.

- Glue

- Something to color with (ie. Pencil crayons, markers etc.)

LEGO DNA Sequencing Activity

1. Prepare a combination of 8 red, green, blue or yellow LEGO bricks, your little scientist, this is

the DNA sequence they need to decipher. Important: The color order is not that important, but

the color of bricks 1, 3, 5 and 7 (starting from the top and progressing down), should not repeat.

This will become important later when arranging the puzzle pieces to form a unique neuron.

2. Explain that each color is associated with a nucleotide letter (ie. Red = T, Blue = A, Yellow =

C, Gray = G).

3. Starting from the top of the LEGO brick tower (the end with the little knobs sticking out) go

brick by brick with your kids, recording the “DNA sequence” on their Neuron Technical Report

sheet.

4. Once their sequence is recorded, have the kids use this sequence to search through all the

possible sequences available. Note: The direction matters. A>G is not the same as A<G. Follow

the order precisely as written on the sequence sheet. For example, if the sequence is A G C T

G A T G, then you will look for the sequences A>G, C>T, G>A, T>G.

5. Once all 4 gene sequences are gathered, have your scientist flip over the pieces and discover

what type of neuron they have. They can now glue these down in their Neuron Technical Report

and color them in.

Follow-Up Activity Idea: Isolating DNA from fruit

If by this point you are still looking for more DNA fun, why not extract some DNA from fruit?

Things required:

Fruit (strawberries or bananas work well)

Cleaning liquid (~5 ml)

Salt (~2 g)

Water (~100 mL)

Isopropyl alcohol (ice cold, ~100 mL)

Hot water (~60 °C)

Coffee filter paper

Two glass jars

Several bowls

A paperclip

Isolating DNA from Fruit Activity

Mash up fruit in bowl (without skins of bananas). In second bowl, mix washing liquid with salt and

water. Avoid creating bubbles. This is the DNA extraction buffer. Add the mashed up fruit to the

extraction buffer and stir as much as possible without creating bubbles. Put the bowl containing the fruit

and extraction buffer into a larger bowl containing hot water (~60 °C) and leave for 15 minutes. After

15 minutes, filter the fruit mixture through a coffee filter to remove the solid material. Carefully drip

the ice-cold isopropyl alcohol down the side of the container into the fruit liquid. This forms a layer of

alcohol on top of the fruit mixture. Between the alcohol and the fruit, a cloud like substance will form.

Using a bent paperclip, slowly draw the DNA up and out of the solution.

Frequently Asked Questions

What is SCOPES Education?

This is a project by two neuroscientist, Dr. Robert Beattie and Dr. Florian Pauler. We created SCOPES

as a fun and interactive way to share our science with students. We strongly believe in the open-source

maker movement and therefore make all files and plans available for free (non-commercial use). Our

goal is to make it easy for scientists all around the world to bring their exciting findings from the lab to

the classroom.

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 let us know using our contact form!

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 popSCOPES case. There is also the environmental aspect and 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.

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 popSCOPES case may not be essential, however, we are convinced it provides

improved didactic user experience and increases 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 made 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? ;)

When will there be more samples on the website?

It is true that right now the number of samples are limited, but we hope to fix this in the very near

future! We plan to incorporate an upload form for scientists in the near future, but if you already have

some samples you want to share with the community, please write to us using our contact form! We

would love to hear from you.

Additional Files Included in this PDF

1. DNAscope Puzzle Pieces (Two pages, print double sided)

2. SCOPES Slides

3. Neuron Technical Report

4. Neuron 1 (Two pages, print double sided)

5. Neuron 2 (Two pages, print double sided)

6. Neuron 3 (Two pages, print double sided)

7. Neuron 4 (Two pages, print double sided)

Acknowledgements

We would also like to thank the IST Austria Events and Communications team for providing multiple

venues for us to develop and present our work. Thank you to the Bioimaging Facility, LSF and PCF at

IST Austria for technical support. Thank you to Happy Lab Wien for access to equipment necessary

for prototyping the SCOPEScase.

Icons for some figures provided by https://pixabay.com/users/mcmurryjulie-2375405/ and image of

mobile devices was adapted from an image by https://pixabay.com/users/nick_h-1821910/.

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