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README.mkd
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README.mkd
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# PlanktonScope Installation
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`pi@raspberrypi:~/retext $ python3 retext.py`
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**Install Raspbian on your Raspberry Pi**
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Download the image
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Download the .zip file of Raspbian Buster with desktop from the Raspberry Pi website Downloads page.
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Writing an image to the SD card
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Download the latest version of balenaEtcher and install it.
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Connect an SD card reader with the micro SD card inside.
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Open balenaEtcher and select from your hard drive the Raspberry Pi .zip file you wish to write to the SD card.
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Select the SD card you wish to write your image to.
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Review your selections and click 'Flash!' to begin writing data to the SD card.
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Prepare your Raspberry Pi
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https://projects.raspberrypi.org/en/projects/raspberry-pi-getting-started/
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Plug the SD Card in your Raspberry Pi
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Connect your Pi to a screen, mouse, keyboard and power
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Finish the setup
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Install the needed libraries for the PlanktonScope
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Make sure you have access to internet and update/upgrade your fresh raspbian :
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Update your Pi first
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sudo apt-get update -y
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sudo apt-get upgrade -y
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Reboot your Pi safely :
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sudo reboot now
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Install CircuitPython
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https://learn.adafruit.com/circuitpython-on-raspberrypi-linux/installing-circuitpython-on-raspberry-pi
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sudo apt-get install python3-pip
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Enable I2C and SPI
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A vast number of our CircuitPython drivers use I2C and SPI for interfacing so you'll want to get those enabled.
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You only have to do this once per Raspberry Pi but by default both interfaces are disabled!
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* Enable I2C
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* Enable SPI
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Once you're done with both :
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sudo reboot now
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Verify you have the I2C and SPI devices with the command :
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ls /dev/i2c* /dev/spi*
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Run the following command to install adafruit_blinka
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pip3 install adafruit-blinka
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Python Installation of MotorKit Library
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Once that's done, from your command line run the following command:
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sudo pip3 install adafruit-circuitpython-motorkit
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Install MotorKit
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https://learn.adafruit.com/search?q=ultimate%20GPS%20HAT
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Check I2C it is working :
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i2cdetect -y 1
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Install Circuit Python :
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sudo pip3 install adafruit-circuitpython-motorkit
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Install RPi Cam Web Interface
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https://elinux.org/RPi-Cam-Web-Interface
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Attach the PiCamera to your Raspberry Pi
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Enable Camera/SSH/I2C in raspi-config
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sudo raspi-config
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Reboot
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sudo reboot now
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Update your RPi :
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sudo apt-get update -y
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sudo apt-get upgrade -y
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Reboot your Pi safely :
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sudo reboot now
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Clone the code from github and enable and run the install script with the following commands:
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git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git
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cd RPi_Cam_Web_Interface
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./install.sh
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Press Enter to allow default setting of the installation
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Press Enter to start RPi Cam Web Interface now
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Found what is the IP of your Raspberry Pi
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sudo ip addr show | grep 'inet 1'
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Reach the url on a local browser : http://127.0.0.1/html/
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Install Ultimate GPS HAT
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Set up the Pi to release the console pins
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https://learn.adafruit.com/adafruit-ultimate-gps-hat-for-raspberry-pi/pi-setup
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Run sudo raspi-config to open up the configuration page and select Interfacing Options :
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Select Serial
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Select NO
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Keep the Serial Port Hardware enabled
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Thats it!
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Shutdown your Pi safely :
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sudo shutdown -h now
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http://www.danmandle.com/blog/getting-gpsd-to-work-with-python/
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Install RGB Cooling HAT
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https://www.yahboom.net/study/RGB_Cooling_HAT
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https://github.com/YahboomTechnology/Raspberry-Pi-RGB-Cooling-HAT
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git clone https://github.com/WiringPi/WiringPi.git
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cd WiringPi
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sudo ./build
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sudo apt-get install gcc
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Download temp_control.zip
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Unzip it in /home/pi/
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cd temp_control/
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Uncomment all lines related to I2C led
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//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x03);
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//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x04);
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//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x02);
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//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x01);
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//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x03);
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gcc -o temp_control temp_control.c ssd1306_i2c.c -lwiringPi
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Install MorphoCut
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https://morphocut.readthedocs.io/en/stable/installation.html
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MorphoCut is packaged on PyPI and can be installed with pip :
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pip install morphocut
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Install MorphoCut server
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https://github.com/morphocut/morphocut-server
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Morphocut server requires Docker Compose, Nodejs and Conda
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Docker Compose
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Installing Docker
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https://withblue.ink/2019/07/13/yes-you-can-run-docker-on-raspbian.html
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Installing Docker CE on Raspbian (Stretch or Buster) for Raspberry Pi is straightforward, and it’s fully supported by Docker. Docker CE is not supported on Raspbian Jessie anymore, so I’d recommend upgrading to a more recent release.
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We’re going to install Docker from the official Docker repositories. While there are Docker packages on the Raspbian repos too, those are not kept up to date, which is something of an issue with a fast-evolving software like Docker.
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To install Docker CE on Raspbian Stretch and Buster:
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Install some required packages first
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sudo apt update -y
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sudo apt install -y apt-transport-https ca-certificates curl gnupg2 software-properties-common
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Get the Docker signing key for packages
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curl -fsSL https://download.docker.com/linux/$(. /etc/os-release; echo "$ID")/gpg | sudo apt-key add -
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Add the Docker official repos
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echo "deb [arch=armhf] https://download.docker.com/linux/$(. /etc/os-release; echo "$ID") \
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$(lsb_release -cs) stable" | \
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sudo tee /etc/apt/sources.list.d/docker.list
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The aufs package, part of the "recommended" packages, won't install on Buster just yet, because of missing pre-compiled kernel modules. We can work around that issue by using "--no-install-recommends"
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sudo apt update
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sudo apt install -y --no-install-recommends \
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docker-ce \
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cgroupfs-mount
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That’s it! The next step is about starting Docker and enabling it at boot:
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sudo systemctl enable docker
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sudo systemctl start docker
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Now that we have Docker running, we can test it by running the “hello world” image:
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sudo docker run --rm arm32v7/hello-world
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If everything is working fine, the command above will output something similar to:
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Output of Docker "hello world" image
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About ARM images
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This should hardly come as a surprise, but there’s a caveat with running Docker on a Raspberry Pi. Since those small devices do not run on x86_64, but rather have ARM-based CPUs, you won’t be able to use all the packages on the Docker Hub.
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Instead, you need to look for images distributed by the arm32v7 organization (called armhf before), or tagged with those labels. Good news is that the arm32v7 organization is officially supported by Docker, so you get high-quality images.
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While the CPUs inside Raspberry Pi 3’s and 4’s are using the ARMv8 (or ARM64) architecture, Raspbian is compiled as a 32-bit OS, so using Raspbian you’re not able to run 64-bit applications or containers.
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Many common applications are already pre-built for ARM, including a growing number of official images, and you can also find a list of community-contributed arm32v7 images on Docker Hub. However, this is still a fraction of the number of images available for the x86_64 architecture.
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Installing Docker Compose
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In this last step we’re installing Docker Compose.
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The official installation method for Linux, as in the Docker documentation, points users to the GitHub downloads page, which however does not offer pre-built binaries for the ARM architecture.
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Luckily, we can still easily install Docker Compose from pip:
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Install required packages
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sudo apt update
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sudo apt install -y python python-pip libffi-dev python-backports.ssl-match-hostname
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Install Docker Compose from pip, this might take a while :
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sudo pip install docker-compose
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With this, you now have a complete Raspberry Pi mini-server running Docker and ready to accept your containers.
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Nodejs
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https://www.instructables.com/id/Install-Nodejs-and-Npm-on-Raspberry-Pi/
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Conda
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https://stackoverflow.com/questions/39371772/how-to-install-anaconda-on-raspberry-pi-3-model-b
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Go and get the latest version of miniconda for Raspberry Pi - made for armv7l processor and bundled with Python 3 (eg.: uname -m)
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wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-armv7l.sh
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md5sum Miniconda3-latest-Linux-armv7l.sh
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bash Miniconda3-latest-Linux-armv7l.sh
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After installation, source your updated .bashrc file with :
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source ~/.bashrc
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Then enter the command,
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python --version
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which should give you :
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Python 3.4.3 :: Continuum Analytics, Inc.
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Install Jupyter Notebook
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https://www.instructables.com/id/Jupyter-Notebook-on-Raspberry-Pi/
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sudo su -
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apt-get update
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apt-get install python3-matplotlib
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apt-get install python3-scipy
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pip3 install --upgrade pip
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reboot
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sudo pip3 install jupyter
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Script to realize an acquisition
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Set color FAN HAT to init
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Get a fix
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Set the pump to fast for x seconds
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Set the pump to super slow
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Set the focus manually
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Click on start
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Set the pump to normal flowrate
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Set the picamera
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Bill of Material
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Items
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Quantity
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Price
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µ-Slide I Luer Variety Pack
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1
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$120
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M12 Lens Set
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1
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$60
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Raspberry Pi 4 Model B
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1
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$62
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Peristaltic Metering Pump with Stepper Motor
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1
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$60
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Adafruit Ultimate GPS HAT Needs the antenna
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1
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$43
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Adapter RMS to M12 x 0.5
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1
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$42
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MicroSD Card 256GB
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1
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$28
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Adafruit DC & Stepper Motor HAT
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1
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$27
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Raspberry Pi Camera Module V2
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1
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$25
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Linear Stepper Motor 12V Focus actuators
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2
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$20
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||||
Yahboom Cooling Fan Hat
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1
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$17
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Adafruit GPS Antenna
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1
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$15
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Power Supply 12V 2A
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1
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$10
|
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Adafruit Power Supply 5.1V 3A - USB C
|
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1
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$10
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Adafruit Hammer Header Male
|
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1
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$7
|
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Adafruit GPIO Ribbon Cable
|
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1
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$3
|
||||
Adafruit GPIO Stacking Header
|
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1
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$2
|
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Female Mount Connector Jack Socket
|
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1
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$1
|
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Switch Accessory, RJ45 Socket
|
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1
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$1
|
||||
Standoff Male to Female 6mm - 2.5mm
|
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8
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$1
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White LED 5mm Ultra Bright
|
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1
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$0
|
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Standoff Male to Female 15mm - 2.5mm
|
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8
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$0
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Machine Screw, M2.5
|
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8
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$0
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6mm thick acrylic - 60cm x 30cm
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1
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$0
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
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sudo apt-get update -y
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sudo apt-get upgrade -y
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|
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|
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sudo apt-get install gpsd gpsd-clients python-gps
|
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-> not installed ion python3.7
|
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pip3 install gps
|
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|
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|
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|
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//test to add the tiny HQ clock (useless if the GPS works)
|
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sudo apt-get install gcc
|
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git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git
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cd RPi_Cam_Web_Interface/
|
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./install.sh
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./stop.sh
|
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|
||||
|
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sudo pip3 install adafruit-circuitpython-motorkit
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||||
|
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pip install morphocut
|
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-> Could not find a version that satisfies the requirement morphocut (from versions: )
|
||||
No matching distribution found for morphocut
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|
||||
|
||||
pip3 install morphocut
|
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-> not installed properly - Read timed out
|
||||
|
||||
|
||||
sudo pip3 install morphocut
|
||||
-> need a better internet
|
||||
|
||||
|
||||
install morphocut server
|
||||
wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-armv7l.sh
|
||||
sudo md5sum Miniconda3-latest-Linux-armv7l.sh
|
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
acq_autoimage_rate
|
||||
acq_camera_name
|
||||
acq_celltype
|
||||
acq_dsp_firmware
|
||||
acq_end
|
||||
acq_flash_delay
|
||||
acq_flash_duration
|
||||
acq_flow_cell_type
|
||||
acq_fluid_volume_imaged
|
||||
acq_id
|
||||
acq_initialization
|
||||
acq_instrument
|
||||
acq_magnification
|
||||
acq_max_esd
|
||||
acq_min_esd
|
||||
acq_mode
|
||||
acq_raw_image_total
|
||||
acq_recalibration_interval_minute
|
||||
acq_sampling_time
|
||||
acq_save_image_file
|
||||
acq_serialno
|
||||
acq_software
|
||||
acq_start
|
||||
acq_stop_reason
|
||||
acq_threshold_black
|
||||
Acq_threshold_light
|
||||
|
||||
|
||||
object_%area
|
||||
object_angle
|
||||
object_area
|
||||
object_area_exc
|
||||
object_bx
|
||||
object_by
|
||||
object_cdexc
|
||||
object_centroids
|
||||
object_circ.
|
||||
object_circex
|
||||
object_compentropy
|
||||
object_compm1
|
||||
object_compm2
|
||||
object_compm3
|
||||
object_compmean
|
||||
object_compslope
|
||||
object_convarea
|
||||
object_convarea_area
|
||||
object_convperim
|
||||
object_convperim_perim
|
||||
object_cv
|
||||
object_date
|
||||
object_depth_max
|
||||
object_depth_min
|
||||
object_elongation
|
||||
object_esd
|
||||
object_fcons
|
||||
object_feret
|
||||
object_feretareaexc
|
||||
object_fractal
|
||||
object_height
|
||||
object_histcum1
|
||||
object_histcum2
|
||||
object_histcum3
|
||||
object_id
|
||||
object_intden
|
||||
object_kurt
|
||||
object_kurt_mean
|
||||
object_lat
|
||||
object_link
|
||||
object_lon
|
||||
object_major
|
||||
object_max
|
||||
object_mean
|
||||
object_meanimagegrey
|
||||
object_meanpos
|
||||
object_median
|
||||
object_median_mean
|
||||
object_median_mean_range
|
||||
object_min
|
||||
object_minor
|
||||
object_mode
|
||||
object_nb1
|
||||
object_nb1_area
|
||||
object_nb1_range
|
||||
object_nb2
|
||||
object_nb2_area
|
||||
object_nb2_range
|
||||
object_nb3
|
||||
object_nb3_area
|
||||
object_nb3_range
|
||||
object_perim.
|
||||
object_perimareaexc
|
||||
object_perimferet
|
||||
object_perimmajor
|
||||
object_range
|
||||
object_skelarea
|
||||
object_skeleton_area
|
||||
object_skew
|
||||
object_skew_mean
|
||||
object_slope
|
||||
object_sr
|
||||
object_stddev
|
||||
object_symetrieh
|
||||
object_symetrieh_area
|
||||
object_symetriehc
|
||||
object_symetriev
|
||||
object_symetriev_area
|
||||
object_symetrievc
|
||||
object_tag
|
||||
object_thickr
|
||||
object_time
|
||||
object_width
|
||||
object_x
|
||||
object_xm
|
||||
object_xmg5
|
||||
object_xstart
|
||||
object_y
|
||||
object_ym
|
||||
object_ymg5
|
||||
object_ystart
|
||||
process_background_method
|
||||
process_esd_max
|
||||
process_esd_min
|
||||
process_gamma_value
|
||||
process_grey_auto_adjust
|
||||
process_id
|
||||
process_lut_offset
|
||||
process_lut_slope
|
||||
process_nb_images
|
||||
process_nb_of_rawfile_images_in_folder
|
||||
process_objects_processed
|
||||
process_pixel
|
||||
process_remove_duplicates
|
||||
process_remove_objects_on_sides
|
||||
process_rolling
|
||||
process_scale
|
||||
process_software
|
||||
process_start_date
|
||||
process_start_time
|
||||
process_stop_after_m_objects
|
||||
process_stop_n_images
|
||||
process_upper
|
||||
sample_barcode
|
||||
sample_comment_or_volume
|
||||
sample_dataportal_descriptor
|
||||
sample_filename
|
||||
sample_id
|
||||
sample_project
|
||||
sample_samplinggear
|
||||
sample_ship
|
||||
sample_volconc
|
||||
sample_volpump
|
||||
Loading…
Reference in a new issue