imzML-Writer 0.0.22

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.

3. (Developer mode) By cloning the Github repo for direct usage.

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

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

Then, open Terminal.app and run the command:

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

Once complete, you should be good to go.

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()

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]