ETH-ScopeM_Hepner

Extract numerical data from bmp image plots

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 the following command:

mamba env create -f environment.yml

• Activate Conda environment:

conda activate Hepner

Your prompt should now start with (Hepner) 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 the following command:

mamba env create -f environment.yml

• Activate Conda environment:

conda activate Hepner

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

Outputs

Plot features are extracted as follow:

- cmap.tif             # colormap (log scale) saved as a `uint8` tif image 
- cmap.csv             # colormap (log scale) saved as a comma separated csv file 
- cmap-raw.tif         # colormap (real values) saved as a `float32` tif image 
- cmap-raw.csv         # colormap (real values) saved as a comma separated csv file 
- line.tif line        # surrounding the colormap saved as a `uint8` tif image
- dot-labels.tif       # labeled dots surrounding the colormap saved as a `uint8` tif image
- dot-info.csv         # dot xy coordinates saved as a comma separated csv file 
- plot.png extracted   # features plot for sanity check saved as png image

Comments