install process for planktoscope segmentation machine

cleanupPlanktoScopeFiles.sh

rm -rf ~/.local/share/planktoscope/data/clean/*
rm -rf ~/.local/share/planktoscope/data/export/*
rm -rf ~/.local/share/planktoscope/data/img/*
rm -rf ~/.local/share/planktoscope/data/objects/*

copyPlanktoScopeImages.sh

rsync -hazv [email protected]:data/img ~/.local/share/planktoscope/data

setup.sh

# ====================================================================
# === install system prerequisites
# ====================================================================
# via package manager
sudo apt install git

# === docker's special install process
# Add Docker's official GPG key:
sudo apt-get update
sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc
# Add the repository to Apt sources:
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
  $(. /etc/os-release && echo "${UBUNTU_CODENAME:-$VERSION_CODENAME}") stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update

# install
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

# ====================================================================
# ====================================================================
# === install forklift
# ====================================================================
# !!! MANUALLY download
# set up install dir
mkdir /opt/forklift
# install
tar -xzf forklift_0.8.0_linux_amd64.tar.gz -C /opt/forklift
# set up symlink for easy usage
sudo ln -s /opt/forklift/forklift /usr/local/bin/forklift
# ====================================================================
# ====================================================================
# === set up docker usage without sudo
# ====================================================================
sudo usermod -aG docker imars  # NOTE: replace `imars` with your username
# !!! MANUALLY log out & log back in
# ====================================================================
# ====================================================================
# === initial set up of segmenter using forklift
# ====================================================================
sudo -E forklift pallet switch --apply github.com/PlanktoScope/pallet-segmenter@edge
# ====================================================================
# ====================================================================
# === set segmenter to run automatically on login
# ====================================================================
echo "forklift stage apply" > ~/.profile
# ====================================================================

USAGE.md

This linux (ubuntu) machine is used to segement images from a planktoScope for submission to EcoTaxa.

To do this:

0. Planktoscope must be on and connected (via wifi)
1. Open a terminal on the desktop (ctrl+alt+t)
2. Type ./copyPlanktoScopeImages.sh and press enter

• this will prompt for the PlanktoScope password.
  • NOTE: nothing will show while typing the password.
• NOTE: use "tab completion" to make this easier
• NOTE: To interrupt a running command press (ctrl+c)

4. Wait for the files to transfer from the PlanktoScope to the desktop
5. Open the Segmenter GUI at http://localhost:1880/ui

• "Update acquisition's folder list" & select image folders
• Click "start segmentation"

8. Once finished, .zip files will be ~/.local/share/planktoscope/data
9. Upload files to EcoTaxa using FTP (filezilla) & use the EcoTaxa website to complete.
   • see the PlanktoScope protocol
10. cleanup files on desktop & planktoscope

• cleanup on desktop by running ~/cleanupPlanktoScopeFiles.sh
• planktoscope files should be managed through the GUI

Other Notes

Re-Segmenting

NOTE: test on 2025-08-06 showed force rework does not force re-segmenting as docs indicate it should. To detect already-segmented images, the segmenter checks for a file in the img directory called done.txt. To force re-segmenting delete done.txt in the relevant img directory.