This package provides functionality to process and visualize mass-spectrometry imaging data.
Currently, it requires your data to be available in the imzML
format.
The full pipeline is also in the process of being developed.
The project is structured in two general parts:
depiction
: implements the whole functionality to process the datadepiction_targeted_preproc
: implements a pipeline that based on some configuration file creates outputs like qc report and .ome.tiff files
This project is in an early state of development. If you are interested, it's best to reach out to us.
Currently, Python 3.12 is required, 3.13 is not compatible yet (missing wheels and e.g. llvmlite).
Install the pyproject.toml
in editable mode, tested with
uv:
uv venv
uv pip install -e ".[dev]"
conda create -n exp-2024-05-depiction python=3.11
conda activate exp-2024-05-depiction
pip install -e ".[dev]"
TODO these are not used consistently everywhere yet
- (2D) Points: (x, y)
- (2D) Images: (y, x, c)
- Sparse images: (i, c)
- Coordinates: (i, d) and each row corresponds to point ordering (i.e. (x, y))
TODO: y-axis direction, xarray conventions (dims, coords, etc.)