Metadata-Version: 2.1
Name: msigen
Version: 0.2.2rc3
Summary: A package for converting spectrometry imaging line scan data files to a visualizable format
Home-page: https://github.com/LabLaskin/MSIGen
License: MIT
Author: Emerson Hernly
Author-email: elhernly@gmail.com
Requires-Python: >=3.9.0,<3.12
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Requires-Dist: ipython (>=8.12.0)
Requires-Dist: multiplierz (==2.2.2)
Requires-Dist: numba (>=0.56.1)
Requires-Dist: numpy (>=1.23.5)
Requires-Dist: opentims_bruker_bridge (>=1.1.0)
Requires-Dist: opentimspy (==1.0.15)
Requires-Dist: pandas (>=2.0.0)
Requires-Dist: pymzml (>=2.5.2,<2.5.7)
Requires-Dist: pywin32 (==306)
Requires-Dist: scikit-image (>=0.19.0)
Requires-Dist: scipy (>=1.10.1)
Requires-Dist: tqdm (>=4.65.0)
Project-URL: Homepage, https://github.com/EmersonHernly/MSIGen
Project-URL: Issues, https://github.com/EmersonHernly/MSIGen/issues
Project-URL: Repository, https://github.com/LabLaskin/MSIGen
Description-Content-Type: text/markdown

# 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 tests 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 tests folder in the Github repository. Open Anaconda Navigator and run Jupyter Notebook in the MSIGen environment. Open "MSIGen_jupyter.ipynb" from Jupyter Notebook. <br><br>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 tests folder in the Github repository. Create a configuration file for your experiment. An example can be found in the tests 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:<br>
[1.] Hernly E, Hu H, Laskin J. MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-brc8d This content is a preprint and has not been peer-reviewed.



