/A_low_cost_imaging_tower

Primary LanguageImageJ MacroApache License 2.0Apache-2.0

A_low_cost_imaging_tower

Intro

A low cost Raspberry pi powered imaging tower and analyses tools for detecting Heterodera schachtii on Arabidopsis thaliana.

lists of requirements to repeat as described in paper

Printing times (Sliced in CURA - 20% infill - PVA Support extruder 2 (BB core) - Default settings)

  1. UMS3_Tower_top < 12h13m
  2. UMS3_Tower_bot < 16h55m
  3. UMS3_Tower_bot_AND_Tower_top < 1d05h30m

Hardware used

  1. Ultimaker S3 with a 0.4 AA and BB core.
  2. Ultimaker tough PLA
  3. Ultimaker PVA
  4. Raspberry pi 4B 4GB RAM
  5. 60 LED STRIP LIGHT 6400K SET IP65 12V (V-TAC)
  6. RPI-HQ-CAMERA(RASPBERRY-PI)
  7. 16mm Telephoto Lens (RASPBERRY-PI)
  8. 30 cm Ribbon Cable (THE PI HUT)
  9. M2 Bolts (RS components)
  10. M2 Nuts (RS components)

Software requirements

  1. Raspberry Pi Imager (to make the raspberry pi bootable disk)
  2. Raspistill (included in Raspberry Pi OS*)
  3. ImageJ (FIJI)
  • Raspistill has been replaced with libcamera-still in the latest Raspberry pi os (Bullseye). Either install a version prior to Bullseye or re-enable legacy camera option in raspi-config.

Contents

This repository contains all the 3D files to make and construct the housing of the components of the imaging tower and scripts to analyse these images.

  1. Image tower 3D files:

    • a: If you own an ultimaker S3 with an AA 0.4 core, PLA and a BB core with PVA, you can use the presliced files: A_low_cost_imaging_tower/Ultimaker S3 CURA sliced/

    • b: If you own another 3D printer, or want to use a printing service, you can use the files in A_low_cost_imaging_tower/STL files/ to generate sliced files for printing.

    Note: the slicing for our files is done in Ultimakers CURA software, which also works for some non Ultimaker printers.

  2. Assembly of the tower.

    • Items needed:
      • RPI-HQ-CAMERA (Raspberry PI)
      • 16mm Telephoto Lens (RASPBERRY-PI)
      • Raspberry PI via a 30 cm Ribbon Cable (THE PI HUT)
      • 60 LED STRIP LIGHT 6400K SET IP65 12V (V-TAC)
    • Assembly instructions for the imaging tower can be found in A_low_cost_imaging_tower/Diagram/Assembly.svg and A_low_cost_imaging_tower/Diagram/compact diagram.svg

  3. Taking the images.

    • Images are taken through the command line using the command metioned in: A_low_cost_imaging_tower/Imaging and Analyses/Imaging command.txt

  4. Analysing images for infection.

    • Depending if coloured agar or standard agar is used the script used for analysing is different. The script is run in imageJ using the interactive interpreter.
      • For coloured agar use: A_low_cost_imaging_tower/Imaging and Analyses/automated_cyst_macro_coloured_agar.ijm
      • For normal agar use: A_low_cost_imaging_tower/Imaging and Analyses/automated_cyst_macro_uncoloured_agar.ijm

  5. Extracting total root surface area.

    • The root surface are of images can be extracted in imageJ using: A_low_cost_imaging_tower/Imaging and Analyses/automated_root_surface_area.ijm