msigen 0.3.1

A package for converting spectrometry imaging line scan data files to a visualizable format

MSIGen

MSIGen is designed for converting mass spectrometry imaging (MSI) data from the raw line-scan data to a visualizable format and is designed with nano-DESI MSI in mind. It has premade files for converting to images using a GUI, jupyter notebook, or from the command line.

Installation on Windows

Using Anaconda (https://www.anaconda.com/download), create a new environment titled "MSIGen" with python >=3.9 and <3.12 and activate it. Then, MSIGen can be installed using the pip package manager.

Run the following in Anaconda Prompt one line at a time:

conda create --name MSIGen python=3.11 -y
conda activate MSIGen
pip install MSIGen

For GUI tool:

Download "make GUI shortcut.py" from the other_files folder in the Github repository. Run this code from Anaconda Prompt.

conda activate MSIGen
python "C:/path/to/make GUI shortcut.py"

After running with the actual location of "make GUI shortcut.py", there should be a shortcut called "MSIGen GUI" on your desktop. This runs the GUI for MSIGen.

For Jupyter Notebook Tool:

Download "MSIGen_jupyter.ipynb" from the other_files folder in the Github repository. Open Anaconda Navigator and run Jupyter Notebook in the MSIGen environment. Open "MSIGen_jupyter.ipynb" from Jupyter Notebook.

Alternatively, Jupyter Notebook can be run from Anaconda Prompt. For the first time opening MSIGen:

conda activate MSIGen
pip install notebook
jupyter notebook

After the first run:

conda activate MSIGen
jupyter notebook

For Command Line Interface Tool:

Download "MSIGen_CLI.py" from the other_files folder in the Github repository. Create a configuration file for your experiment. An example can be found in the other_files folder. Run the following in Anaconda Prompt:

conda activate MSIGen
python "C:/Path/to/MSIGen_CLI.py" "C:/path/to/config_file1.json" "C:/path/to/config_file2.json"

Supply one configuration file for each dataset to be processed.

Referencing

If MSIGen was used in your project, please reference it using the following:
[1.] Hernly E, Hu H, Laskin J. MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data. J. Am. Soc. Mass Spectrom. 2024, 35, 10, 2315–2323; doi:10.1021/jasms.4c00178