imzML-Writer 1.0.0

"User friendly writing of imzML mass spectrometry imaging files from continuous MSI data"

Installation:

Installing imzML Writer has gotten easier! We're now available as:

1. (Recommended) As a python package available from pip:

pip install imzml-writer

2. (Experimental) Standalone app bundles / executables for Mac and PC in the builds folder of the Github.

Installation:

Using imzML Writer depends on msconvert for conversion of raw vendor files to the open format mzML. On PC, this can be installed normally from Proteowizard: https://proteowizard.sourceforge.io/download.html

imzML Writer will prompt you for the path to msconvert the first time you try to convert raw files (see Docs), or you can add msconvert to the system path if you'd like to run msconvert from the command line.

On Mac, you can still run msconvert via a docker image. First, install Docker: https://www.docker.com/products/docker-desktop/

Similarly, imzML Writer will prompt you to download the docker image the first time you try to call it. If you'd like to do this in advance you can open Terminal.app and run the command:

docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

Quickstart

Once the python package (pip install imzML-Writer) and msconvert (or the docker image) have been successful installed, you can quickly launch the GUI with the script:

import imzML_Writer.imzML_Writer as iw

iw.gui()

Compatibility

Software	Functioning?	Comments
Cardinal MSI	Yes
METASPACE	Yes
M2aia	Yes
MSIReader	Yes
Julia mzML_imzML	Yes
SCiLS Lab	Yes	Must specify pixel dimensions
Mozaic	No	Work in Progress

Documentation

Detailed installation instructions, quickstart guides, and documentation are available on the ReadTheDocs page: https://imzml-writer.readthedocs.io/en/latest/

Contact us

Please direct any questions, concerns, or feature requests to me at [e-mail]