imzy 0.2.0

imzy: A new reader interface to imzML and other imaging mass spectrometry formats.

imzy

imzy: A simple reader interface to imzML, Bruker (.tdf/.tsf) file formats

Getting started

Install using pip

pip install imzy

Analyse your data

import numpy as np
from imzy import get_reader

# we currently support imzML, Bruker .d (.tsf/.tdf) formats
reader = get_reader(PATH_TO_FILE)
# will extract mass spectrum for pixel index '0'
mz_x, mz_y = reader.get_mass_spectrum(0)
# will extract summed mass spectrum for pixel indices 0-100
mz_x, mz_y = reader.get_summed_spectrum(np.arange(100))
# iterate over all mass spectra in the dataset
for mz_x, mz_y in reader.spectra_iter():
  ...
# get tic array
tic = reader.get_tic()
# this array is 1d so needs to be reshaped to 2d if you want to view it as an image
tic = reader.reshape(tic)
# will extract the 885.549 ion image with 10 ppm window around it
image = reader.get_ion_image(885.549, ppm=10)
# you can also extract multiple images at the same time (which is much more efficient since the spectra
# only need to be loaded into memory once)
mzs = [...] # list of m/zs to extract
images = reader.get_ion_images(mzs, tol=0.05)

Planned features

• add functionality to readers
• improve performance
• improve tests
• add better caching support
• add support for Waters (.raw) files
• add support for Thermo (.raw) files

Contributing

Initialize your code

1. Initialize git inside your repo:

cd imzy && git init

2. Create conda environment. We are using imzy as its name.

conda create -n imzy python=3.9

3. Initialize and install pre-commit hooks:

make develop
make pre-commit-install

4. Run the codestyle:

make codestyle

5. Upload initial code to GitHub:

git add .
git commit -m ":tada: Initial commit"
git branch -M main
git remote add origin https://github.com/imzy/imzy.git
git push -u origin main

🛡 License

This project is licensed under the terms of the BSD-3 license. See LICENSE for more details.

📃 Citation

@misc{imzy,
  author = {imzy},
  title = {imzy: A new reader/writer interface to imzML and other imaging mass spectrometry formats.},
  year = {2022},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/imzy/imzy}}
}