m2aia / pym2aia

pyM²aia is a Python package for memory-efficient access and processing of mass spectrometry image data. The I/O functionality is derived from the interactive desktop application M²aia. Special features are the batch generator utilities for deep learning applications.

Downloads

M²aia: a mass spectrometry imaging applications for interactive analysis in MITK

M²aia is open source software, based on the well-known Medical Imaging Interaction Toolkit (MITK). The software enables interactive visualization, signal-processing, 3D reconstruction and multi-modal image registration of mass spectrometry imaging (MSI) datasets.

More information

github.io/m2aia
Build instructions (windows/Linux)
Protocols

Cite M²aia

Cordes J; Enzlein T; Marsching C; Hinze M; Engelhardt S; Hopf C; Wolf I (July, 2021): M²aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data https://doi.org/10.1093/gigascience/giab049

biotools:m2aia

Docker

To use M²aia in a browser run:

docker pull ghcr.io/m2aia/m2aia:latest
docker run --rm -v /local/data/path:/data -p 8888:80 ghcr.io/m2aia/m2aia:latest

with password:

docker run --rm -v /local/data/path:/data -e VNC_PASSWORD=<password> -p 8888:80 ghcr.io/m2aia/m2aia:latest

Start M²aia by accessing http://localhost:8888

The container will shut down if M²aia is closed (File->Exit). The results written to the mapped volume have root user ownership

Python

We provide ImzML Reader and the Signal Processing utilities for Python.

https://github.com/m2aia/pym2aia
https://github.com/m2aia/pym2aia-examples

Contact

If you have questions about the application or if you would like to give us feedback, don't hesitate to open a new issue or contact me directly.

pym2aia's Issues

Metadat handling in pym2aia

Hi, i've noticed something about the .GetMetaData() function. It only returns the "name" parameter, and not the "value" parameter. I'm assuming that the metadata values get lost somewhere in the transition between Python and C++, because the m2aiaCore soure code looks like it is aware of them.
I'm including a minimal example below:

When calling .GetMetaData() on a ImzMLReader, i get the following list (shortend for overview) with strings:
"[...,'pixel size x', 'pixel size y', 'pixel size z', 'scanSettings0.horizontal line scan', 'scanSettings0.linescan right left', ...]"

My imzMl file looks like this:

scanSettingsList count="1">
scanSettings id="scanSettings0">
cvParam accession="IMS:1000046" cvRef="IMS" name="pixel size x" value="50"/>"
cvParam accession="IMS:1000047" cvRef="IMS" name="pixel size y" value="50"/>"
cvParam accession="IMS:1000490" cvRef="IMS" name="linescan right left"/>"
cvParam accession="IMS:1000480" cvRef="IMS" name="horizontal line `scan"/>"

Is there a way th make the GetMetaData() output into a dictionary with a name and value pair? or any other way to access the value from within pym2aia?

Bring the package back onto pypi

Seems like the package is no longer available on pypi.

https://pypi.org/search/?q=pym2aia&o=

Handling of XAxisDepthwith processed imzML files

Hi, i've encountered a behavior i do not fully understand and i had a few questions regarding the XAxisDepth() method and other fuctions (in particular .GetXAxis() and .GetMeanSpectrum() ) when i am working with processed imzML files.

When i use XAxisDepth() on the ImzMLReader, it binns the spectra to an axis. To check how well this performed, i plotted the Depth of each mass-axis in the file against the pixel index. But somehow, i do not see a correlation between the number of bins used for the averaging and the acutal depths of the spectra. see below for the plot:

is there a way to specify how much bins the averaging should take or how large they should be?

also, colsely related to this, i observed that the binned mz values from .GetMeanSpectrum are somewhat shifted from the original processed data. I think this is also related to the binsize, since the algorithm seems to anticipate to large bins for my data and the background peaks disturb the weighted average of the mean spectrum.
to illustrate this, i also plottet the raw data of a small set of points over the averaged spectrum from this set (see below)

tl,dr: Is there a way to send a binsize or a number of bins to the underlying averaging function when XAxisDepth() is called?

Segmentation fault due to missing interface definition of GetOrigin()

Add writer for continuous centroid imzML files

Write a continuous centroid imzML file by providing a list of centroids