TagLab: an image segmentation tool oriented to marine data analysis

|   Software Requirements   |   Install   |   Update   |   Citation   |

Introduction

TagLab was created to support the activity of annotation and extraction of statistical data from ortho-maps of benthic communities. The tool includes different types of CNN-based segmentation networks specially trained for agnostic (relative only to contours) or semantic (also related to species) recognition of corals. TagLab is an ongoing project of the Visual Computing Lab.

Warning ⚠️

This is a developmental fork from the original repository; changes are made here, like, really frequently... proceed with caution.

✨ New Features:

• 10/2023
  • Install script for Windows using Anaconda; see Installation instructions below
  • Segment Anything Model (SAM)
    • Predictor for one-click segmentations
    • Generator for automatic segmentations
• 12/2023
  • Width and Height of current view is shown in top-right (updates w/ zoom)
  • Users can mark grid cells as complete from within SAM and pos/neg (RITM) tools
  • Working area for SAM and pos/neg (RITM) tools will show you the dimensions of the working area
• 02/2024
  • iView using Metashape API to view corresponding images of orthomosaic; requires Professional license
  • Fixed Refine tool bug
  • Point annotations (all credit goes to original TagLab authors)
    • Point sampling select work area (shows pixel and metric space)
    • Basic Import / Export of point annotations in CoralNet Format
• 03/2024
  • Integrated Upload and API tools from CoralNet Toolbox into TagLab to allow for CoralNet models to make predictions on point annotations in orthomosaic.

We are working hard to create a website with detailed instructions about TagLab. Stay tuned(!)

Software Requirements

TagLab runs on Linux, Windows, and MacOS. To run TagLab, the main requirement is just 64bit Python 3.8.x, 3.9.x or 3.10.x.

GPU accelerated computations are not supported on MacOS and on any machine that has not an NVIDIA graphics card. To use them, you'll need to install the NVIDIA CUDA Toolkit, versions 10.2, 11.3, 11.6 and 11.7 are supported. If you don't have a NVida graphics card (or if you use MacOS), CPU will be used.

Installing TagLab

To install TagLab on Windows using Anaconda, follow the instructions below. If CUDA is not installed on your computer, include cpu when running the install script:

# Anaconda Command Prompt

# Create a conda environment for TagLab
conda create --name taglab python=3.8 -y

# Activate the environment
conda activate taglab

# Within the TagLab folder, run the install_conda_windows.py script
python install_conda_windows.py [cpu]

# Run TagLab
python Taglab.py

For further instructions on installing TagLab see below.

Step 1: Install Anaconda

1. Download Anaconda:
   • Go to the Anaconda website.
   • Download the appropriate version for your Windows system (e.g., 64-bit or 32-bit).
   • Follow the installation instructions provided on the website.

Step 2: Open Anaconda Command Prompt

1. Search for Anaconda Command Prompt:
   • Press the Windows key on your keyboard.
   • Type "Anaconda Command Prompt" and press Enter.

Step 3: Create a Conda Environment for TagLab

1. Create a new conda environment:
   • In the Anaconda Command Prompt, type the following command and press Enter:

     conda create --name taglab python=3.8 -y

   • This command creates a new conda environment named "taglab" with Python version 3.8.

Step 4: Activate the Conda Environment

1. Activate the conda environment:
   • Type the following command and press Enter:

     conda activate taglab

   • Your command prompt should now show that you are in the "taglab" environment.

Step 5: Download TagLab and Install Dependencies

1. Navigate to the TagLab folder:

   • Download this TagLab fork .
   • Extract the contents of the downloaded zip file to a location on your computer.
   • Open the Anaconda Command Prompt and navigate to the folder where TagLab is extracted, using the cd command. For example:

     cd path\to\Taglab

2. Run the installation script:

   • Type the following command and press Enter:

     python install_conda_windows.py [cpu]

     • Replace [cpu] with nothing if CUDA is installed on your computer, or include cpu if CUDA is not installed.
     • This script installs the necessary dependencies for TagLab.

Step 6: Run TagLab

1. Run TagLab:
   • After the installation is complete, you can run TagLab using the following command:

     python Taglab.py

   • This command starts TagLab, and you should now be able to use the tool within the activated conda environment.

Citation

If you use TagLab, please cite it.

@article{TagLab,
	author = {Pavoni, Gaia and Corsini, Massimiliano and Ponchio, Federico and Muntoni, Alessandro and Edwards, Clinton and Pedersen, Nicole and Sandin, Stuart and Cignoni, Paolo},
	title = {TagLab: AI-assisted annotation for the fast and accurate semantic segmentation of coral reef orthoimages},
	year = {2022},
	journal = {Journal of Field Robotics},
	volume = {39},
	number = {3},
	pages = {246 – 262},
	doi = {10.1002/rob.22049}
}