.. _install: ========================== PlanktonScope Installation ========================== comment the line before the cmd line :: pi@raspberrypi:~/retext $ python3 retext.py Install Raspbian on your Raspberry Pi =================== Download the image Download the .zip file of Raspbian Buster with desktop from the Raspberry Pi website Downloads page. Writing an image to the SD card Download the latest version of balenaEtcher and install it. Connect an SD card reader with the micro SD card inside. Open balenaEtcher and select from your hard drive the Raspberry Pi .zip file you wish to write to the SD card. Select the SD card you wish to write your image to. Review your selections and click 'Flash!' to begin writing data to the SD card. Prepare your Raspberry Pi https://projects.raspberrypi.org/en/projects/raspberry-pi-getting-started/ Plug the SD Card in your Raspberry Pi Connect your Pi to a screen, mouse, keyboard and power Finish the setup Install the needed libraries for the PlanktonScope Make sure you have access to internet and update/upgrade your fresh raspbian Update your Pi first :: sudo apt-get update -y sudo apt-get upgrade -y Reboot your Pi safely :: sudo reboot now Raspberry Pi configurations ================== Enable Camera/SSH/I2C in raspi-config Open up the configuration page and select Interfacing Options by typing this command: :: sudo raspi-config Select Serial Select NO Keep the Serial Port Hardware enabled Reboot your Pi safely :: sudo reboot now Install CircuitPython ================== https://learn.adafruit.com/circuitpython-on-raspberrypi-linux/installing-circuitpython-on-raspberry-pi Run the following command to install adafruit_blinka :: pip3 install adafruit-blinka sudo pip3 install adafruit-circuitpython-motorkit Install RPi Cam Web Interface ================== https://elinux.org/RPi-Cam-Web-Interface Clone the code from github and enable and run the install script with the following commands :: git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git cd RPi_Cam_Web_Interface ./install.sh Press Enter to allow default setting of the installation Press Enter to start RPi Cam Web Interface now Found what is the IP of your Raspberry Pi :: sudo ip addr show | grep 'inet 1' Reach the url on a local browser : http://127.0.0.1/html/ Install Ultimate GPS HAT ================== https://learn.adafruit.com/adafruit-ultimate-gps-hat-for-raspberry-pi/pi-setup http://www.danmandle.com/blog/getting-gpsd-to-work-with-python/ Install RGB Cooling HAT ================== https://www.yahboom.net/study/RGB_Cooling_HAT https://github.com/YahboomTechnology/Raspberry-Pi-RGB-Cooling-HAT :: git clone https://github.com/WiringPi/WiringPi.git cd WiringPi sudo ./build sudo apt-get install gcc Install Node-RED ================== https://nodered.org/docs/getting-started/raspberrypi Type this command :: bash <(curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered) Install MorphoCut ================== https://morphocut.readthedocs.io/en/stable/installation.html MorphoCut is packaged on PyPI and can be installed with pip :: pip install morphocut Install MorphoCut server ------------------ https://github.com/morphocut/morphocut-server Morphocut server requires Docker Compose, Nodejs and Conda Docker Compose ------------------ Installing Docker ------------------ https://withblue.ink/2019/07/13/yes-you-can-run-docker-on-raspbian.html 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. 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. To install Docker CE on Raspbian Stretch and Buster: Install some required packages first :: sudo apt update -y sudo apt install -y apt-transport-https ca-certificates curl gnupg2 software-properties-common Get the Docker signing key for packages :: curl -fsSL https://download.docker.com/linux/$(. /etc/os-release; echo "$ID")/gpg | sudo apt-key add - Add the Docker official repos :: echo "deb [arch=armhf] https://download.docker.com/linux/$(. /etc/os-release; echo "$ID") $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list 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" sudo apt update sudo apt install -y --no-install-recommends \ docker-ce \ cgroupfs-mount That’s it! The next step is about starting Docker and enabling it at boot: sudo systemctl enable docker sudo systemctl start docker Now that we have Docker running, we can test it by running the “hello world” image: sudo docker run --rm arm32v7/hello-world If everything is working fine, the command above will output something similar to: About ARM images ------------------ 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. 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. 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. 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. Installing Docker Compose In this last step we’re installing Docker Compose. 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. Luckily, we can still easily install Docker Compose from pip: Install required packages ------------------ sudo apt update sudo apt install -y python python-pip libffi-dev python-backports.ssl-match-hostname Install Docker Compose from pip, this might take a while : sudo pip install docker-compose With this, you now have a complete Raspberry Pi mini-server running Docker and ready to accept your containers. Nodejs ------------------ https://www.instructables.com/id/Install-Nodejs-and-Npm-on-Raspberry-Pi/ Conda ------------------ https://stackoverflow.com/questions/39371772/how-to-install-anaconda-on-raspberry-pi-3-model-b Go and get the latest version of miniconda for Raspberry Pi - made for armv7l processor and bundled with Python 3 (eg.: uname -m) wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-armv7l.sh md5sum Miniconda3-latest-Linux-armv7l.sh bash Miniconda3-latest-Linux-armv7l.sh After installation, source your updated .bashrc file with : source ~/.bashrc Then enter the command, python --version which should give you : Python 3.4.3 :: Continuum Analytics, Inc. Install Jupyter Notebook ================== https://www.instructables.com/id/Jupyter-Notebook-on-Raspberry-Pi/ sudo su - apt-get update apt-get install python3-matplotlib apt-get install python3-scipy pip3 install --upgrade pip reboot sudo pip3 install jupyter Script to realize an acquisition Set color FAN HAT to init Get a fix Set the pump to fast for x seconds Set the pump to super slow Set the focus manually Click on start Set the pump to normal flowrate Set the picamera Bill of Material Items Quantity Price µ-Slide I Luer Variety Pack 1 $120 M12 Lens Set 1 $60 Raspberry Pi 4 Model B 1 $62 Peristaltic Metering Pump with Stepper Motor 1 $60 Adafruit Ultimate GPS HAT Needs the antenna 1 $43 Adapter RMS to M12 x 0.5 1 $42 MicroSD Card 256GB 1 $28 Adafruit DC & Stepper Motor HAT 1 $27 Raspberry Pi Camera Module V2 1 $25 Linear Stepper Motor 12V Focus actuators 2 $20 Yahboom Cooling Fan Hat 1 $17 Adafruit GPS Antenna 1 $15 Power Supply 12V 2A 1 $10 Adafruit Power Supply 5.1V 3A - USB C 1 $10 Adafruit Hammer Header Male 1 $7 Adafruit GPIO Ribbon Cable 1 $3 Adafruit GPIO Stacking Header 1 $2 Female Mount Connector Jack Socket 1 $1 Switch Accessory, RJ45 Socket 1 $1 Standoff Male to Female 6mm - 2.5mm 8 $1 White LED 5mm Ultra Bright 1 $0 Standoff Male to Female 15mm - 2.5mm 8 $0 Machine Screw, M2.5 8 $0 6mm thick acrylic - 60cm x 30cm 1 $0 sudo apt-get update -y sudo apt-get upgrade -y sudo apt-get install gpsd gpsd-clients python-gps -> not installed ion python3.7 pip3 install gps //test to add the tiny HQ clock (useless if the GPS works) sudo apt-get install gcc git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git cd RPi_Cam_Web_Interface/ ./install.sh ./stop.sh sudo pip3 install adafruit-circuitpython-motorkit pip install morphocut -> Could not find a version that satisfies the requirement morphocut (from versions: ) No matching distribution found for morphocut pip3 install morphocut -> 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 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