Processing of mass spectrometry imaging and micro X-Ray fluorescence data.
Project description
Mass Spectrometry Imaging Workflow (maspim
)
maspim
is a python package that allows users to read, process and interpret mass spectrometry imaging (MSI) data from Bruker instruments.
This package implements methods to process mass spectra, combine them with image information or other measurements (such as micro X-Ray fluorescence, µXRF) and special functionality for laminated sediments to combine spectra in the same layers.
Prerequisites
Before you begin, ensure you have met the following requirements:
-
You have a version of
python3
installed (preferentially the up-to-date version) -
You have
R
installed -
You have the
R
packagertms
installed
You may also want to check out msiAlign, which is not directly a prerequisite, but useful for setting the punch-holes when the automatic detection fails and msi_feature_extraction if you want to work with exported txt files from DataAnalysis.
Installing maspim
maspim
is now on PyPI.
pip install maspim
Also, checkout our github page for the up-to-date version and additional resources.
To get the freshest version, run
pip install git+https://github.com/yaza11/maspim.git
in your console (assuming you have pip installed).
Using maspim
This is just a quick overview. For more comprehensive tutorials please have a look at the Notebooks.
Generally it is advised to stick to the objects provided at the top level of maspim
, which are
-
ProjectMSI
andProjectXRF
to manage MSI and µXRF measurements respectively and fetched with theget_project
function -
ImageSample
,ImageROI
andImageClassified
to set photo properties and finding the sample area -
Transformation
to register images -
ReadBrukerMCF
andhdf5handler
for reading and storing data files. -
Spectra
to extract intensities from the mass spectra -
MSI
andXRF
for handling MSI and µXRF measurements. -
XRay
for adding information from an X-Ray -
AgeModel
to set an age model
and a few others. ProjectMSI
and ProjectXRF
are the core objects of this package, which manage most of the aforementioned objects. So unless you have a very specific application in mind, it is recommended to do everything with the methods provided by ProjectMSI
and ProjectXRF
.
Let's look at a short example of how to define the ${U_{37}^{k}}^\prime$ proxy, which you can use to check that your installation worked.
from maspim import get_project
from maspim.res.compound_masses import mC37_2, mC37_3
p = get_project(is_MSI=True, path_folder='path/to/your/measurement.i', is_laminated=False)
# sets or loads ImageHandler, ImageSample, ImageROI and ImageClassified
p.require_images()
# perform all steps to extract intensities from alkenones
p.set_spectra(targets=[mC37_2, mC37_3], suppress_warnings=True)
p.set_data_object()
p.add_pixels_ROI()
# we did not provide any ages, so a time series does not make much sense, but
# this is just a test, so don't try to interpret the results
p.set_time_series(average_by_col='x', is_continuous=True)
p.set_UK37(method_SST='prahl', n_successes_required=0)
# we can use the index instead of the age for now
p.uk37_proxy.feature_table.loc[:, 'age'] = p.uk37_proxy.feature_table.x
# you should see a plot after this
p.uk37_proxy.plot_comp('SST', errors=False)
Contributing to maspim
If you find any bugs or missing features, you are welcome to contribute to maspim
, just follow these steps:
-
Fork this repository.
-
Create a branch:
git checkout -b <branch_name>
. -
Make your changes and commit them:
git commit -m '<commit_message>'
-
Push to the original branch:
git push origin <project_name>/<location>
-
Create the pull request.
Alternatively see the GitHub documentation on creating a pull request.
Contributors
Thanks to @weimin-liu who has contributed to this project.
Contact
Feel free to reach out at me via yzander@marum.de.
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