img_header can be used for Jeol1400 images to read out tif properties like the pixelsize. The pixelsize can be used for setting the scale in Fiji (ImageJ).
Install anaconda (for better version control). Therefore follow the instructions here. ATTENTION:: During installation, make sure to add Anaconda to your PATH variable.
Generate a new python environment using anaconda. Inside a terminal type:
conda create -n ENVNAME python=3.9
for example, you can name the environment img_header by creating an environment with
conda create -n img_header python=3.9
Next, you need to activate the conda environment by typing
conda activate img_header
Install pip inside the conda environment (this is a package manager for python packages)
conda install pip
Now, you are able to install all dependencies using pip. Therefore type:
pip install -r requirements.txt
Now you should be all setup to run the script by
python Main.py --path PATH_TO_IMG
- Open Terminal
- Open img_header. Example: If img_header is installed on desktop: cd "path to file" Tipp: write cd, drag and drop img_header folder into Terminal
- Activate conda: conda activate img_header
- Read out tif properties: python Main.py --path "path to image" Tipp: Drag and drop Jeol1400 image into Terminal instead of write path manual.
- At the end deactivate conda: conda deactivate
- Open Image in Fiji
- Analyse - Set Scale: Distance in pixels: 1 Known distance: pixelsize from img_header in nm Unit of length: nm
- Analyse - Tools - Scale bar