BDehapiot/ETH-ScopeM_Meschichi

3D segmentation of plant nuclei sub-domains

ETH-ScopeM_Meschichi

3D segmentation of plant nuclei sub-domains

Index

• Installation
• Outputs
• Comments

Installation

Pease select your operating system

Windows

Step 1: Download this GitHub Repository

• Click on the green <> Code button and download ZIP
• Unzip the downloaded file to a desired location

Step 2: Install Miniforge (Minimal Conda installer)

• Download and install Miniforge for your operating system
• Run the downloaded .exe file
  • Select "Add Miniforge3 to PATH environment variable"

Step 3: Setup Conda

• Open the newly installed Miniforge Prompt
• Move to the downloaded GitHub repository
• Run one of the following command:

# TensorFlow with GPU support
mamba env create -f environment_tf_gpu.yml
# TensorFlow with no GPU support 
mamba env create -f environment_tf_nogpu.yml

• Activate Conda environment:

conda activate Meschichi

Your prompt should now start with (Meschichi) instead of (base)

MacOS

Step 1: Download this GitHub Repository

• Click on the green <> Code button and download ZIP
• Unzip the downloaded file to a desired location

Step 2: Install Miniforge (Minimal Conda installer)

• Download and install Miniforge for your operating system
• Open your terminal
• Move to the directory containing the Miniforge installer
• Run one of the following command:

# Intel-Series
bash Miniforge3-MacOSX-x86_64.sh
# M-Series
bash Miniforge3-MacOSX-arm64.sh

Step 3: Setup Conda

• Re-open your terminal
• Move to the downloaded GitHub repository
• Run one of the following command:

# TensorFlow with GPU support
mamba env create -f environment_tf_gpu.yml
# TensorFlow with no GPU support 
mamba env create -f environment_tf_nogpu.yml

• Activate Conda environment:

conda activate Meschichi

Your prompt should now start with (Meschichi) instead of (base)

Outputs

nData.csv - nuclei data

# Nuclei data
    - nLabel    # IDs
    - nVolume   # volume (µm3)  
    - nCtrd     # centroid coords (zyx)
    - nMajor    # fitted ellipse major axis length (µm)
    - nMinor    # fitted ellipse minor axis length (µm)
    - nMMRatio  # minor / major axis ratio

# Associated chromocenters data
    - n_cLabel  # associated chromocenter IDs
    - n_cNumber # number of cromocenters
    - n_cVolume # cumulative volume of chromocenters (µm3)
    - n_cnRatio # chromocenter / nuclei volume ratio

cData.csv - chromocenters data

# Chromocenters data data
    - cLabel    # IDs
    - nVolume   # volume (µm3)  
    - cCtrd     # centroid coords (zyx)
    - cMajor    # fitted ellipse major axis length (µm)
    - cMinor    # fitted ellipse minor axis length (µm)
    - cMMRatio  # minor / major axis ratio
    - cInt      # intensity mean (raw intensities)
    - cEDMb     # distance from nucleus periphery (µm)
    - cEDMc     # distance from nucleus centroid (µm)

# Associated nuclei data
    - c_nLabel  # associated nucleus ID

Comments

Meeting 24/05/2024

• Quantifications
  • number of chromocenters (done)
  • volume of nuclei, chromocenters and ratio (done)
  • brightness of chromocenters DAPI (background substraction ?) (done)
  • shape descriptors (nuclei & chromocenters) (done)
  • distance nuclei border vs. chromocenter centroid (done)
  • distance nuclei centroid vs. chromocenter centroid (done)
  • statistics (avg, variance, std...)
• Other
  • create a remote folder (done)