Collection of useful scripts and python code for mask generation, data extraction and plotting etc. The workflow typically uses the following files in the order below:
MCD to TIFF: Jupyter notebook that uses the Bodenmiller lab's IMCtools python package to generate tiff files from a .zip file of IMC data.
Cell Mask Generator: ImageJ macro that takes a highly multiplexed tiff image (such as that generated by Imaging mass cytometry), and walks you through generating a multichannel .tif file where each channel contains a binary image of a single cell. This can be used for masking in automated data extraction on a per-egg basis.
TIFF to dataframes: Jupyter notebook that takes multichannel tiffs and uses ImageJ-generated mask files to extract total signal on a per-cell, per-channel basis, saving the data in pandas dataframes.
Quality Control: Jupyter notebooks for exploring and checking quality of post-masking images to ensure data extraction is not capturing non-specific signal. Interactive Plotting notebook takes tiff images and masks, plus the long dataframe generated by TIFF to dataframes, and produces an interactive graph displaying the cell each datapoint refers to on hover.