Here are the packages this course will use:
tifffile: tiff import and export
pandas: dataframe manipulation
numpy: multidimensional arrays
matplotlib: standard plotting package including image viewing
scipy ndimage: core image processing tools including label comprehension
How to install the packates with conda:
Create and environment called ipenv:
conda create -n ipenv python=3.8
Activate the environment:
conda activate ipenv
Optional: set ipykernel in jupyter:
pip install --user ipykernel
python -m ipykernel install --user --name=ipenv
Install packages:
conda install -c conda-forge jupyter numpy pandas scipy matplotlib tifffile pillow
Alternative: To install from environment.yml file (environment will be called ipenv):
conda env create -f environment.yml
The notebook image_processing_basics.ipynb is the starting place for the course and talks about pixels and image display in python.
The notebook image_label_measurements.ipynb talks about segmenting and labeling image objects and performing measurements on them.
Image sources: the images are from https://imagej.nih.gov/ij/images. They have been made into tif files for easy import.