Fluorescence Microscope

3D Printed, Raspberry Pi and Arduino-Controlled Fluorescence Microscope

This page serves as a guide to the steps taken to setup the Flypi microscope.

Step 1: Set up the Pi by downloading NOOBS/Raspbian OS... (This will take a decent amount of time ~ 20 minutes). Once finished, set up your pi by walking through the "Welcome to Raspberry Pi" screen.

Username: pi

Password: microscope

Once you're finished being welcomed to the world of Raspberry Pi, the Pi will restart.

Step 2: Once connected to a Wifi network, open up a terminal. Type the following commands into the terminal:

sudo apt-get update

sudo apt-get upgrade

Step 3: Download the Arduino IDE.

Type the following command into the terminal window:

sudo apt-get install arduino

Step 4: We will also need some libraries for the LED Ring and LED Matrix we are using. Links to these can be found at the Github Page. While you are here, you can download the zip of this Git repository buy clicking on the green clone or download button. Once downloaded, you should extract this folder to your desktop. The folder should be found in your Downloads folder. If you right click on the zip file, then you should receive the option to extract to a location.

You should repeat this procedure for the two Arduino Libraries mentioned above. You will then have to import those libraries into the sketchbook so Arduino recognizes them. To do this, you must extract them, to whatever location. Then rename (right click, rename) to something that doesn't include any hyphens or the word master. You can then import these folders by opening the Arduino IDE and selecting Sketch --> Import Library... --> Add Library...

Step 5: Type another command into the terminal in order to install the library needed to convert PiCamera output to .avi videos. The command is:

sudo apt-get install libav-tools

also install guac library using:

sudo apt-get update

sudo apt-get install gpac

Step 6: We need to edit the Raspberry Pi Configuration in order for our code to work. This is done by clicking on the Raspberry in the upper left portion of the screen --> Preferences --> Raspberry Pi Configuration. Here we will select the Interfaces tab. We will then enable the Camera, Serial Port, Serial Console, and 1-Wire. This will require the Pi to reboot.

Step 7: Once everything is installed, you should be able to run the GUI using the following commands in a terminal:

cd ~/Desktop/Flypi-master/Python/

sudo python3 ./run.py

Step 8: