Welcome to Alchromy! This package is designed to perform spectral deconvolution on waveforms obtained from UV-Vis spectrometry. It was designed for identification of different hemoglobin species in complex mixtures. It is currently in a closed beta testing phase, so expect many changes going forward.
Alchromy requires Python 3 and the following packages (install with pip or your favorite IDE):
tkinter pandas glob scipy numpy matplotlib xlrd
Users can access the script through the command line (using deconv_multi.py) or the GUI (main_gui.py). In either case, the following parameters should be specified:
- Data file: A file path, or list of file paths (directory if using GUI), in which the experimental waveforms are located.
- Reference file: A file path to a sheet of waveforms to be used as pure reference spectra for deconvolution. Defaults to refspec.dat.
- Ignored species: Waveforms from the reference that should not be used in curve fitting.
- nm_min and nm_max: Minimum and maximum wavelengths to consider for the curve fitting. Both experimental and reference spectra must have values continuously in this region.
- Kinetic vs Replicate: If more than one column of data is present, specify whether it should be treated as kinetic data collected over time, or replicates of the same sample (where the spectra will be averaged).
- Normalize: Adjusts the input waves such that the lowest value becomes 0. Potentially helpful for solutions with known baseline offset from light scattering, use with caution otherwise.
- File note (optional): A short string that will be appended to the file name and included in the text report. Useful for reporting concentration, operator ID, additional sample information, etc.
- Verbose Output: If enabled, will print frequent status updates to your Python console.
- Graph, Report, and Spectra: Boolean values that determine whether .png, .txt, and .xlsx files (respectively) are produced.
The file input methods of Alchromy are being expanded, but are currently limited to a narrow specification. Reference files should contain multiple columns beginning with wavelength. Subsequent columns should be named for the species they contain. Experimental data files should have a list of wavelengths as the first column. Each subsequent column will be treated as either replicates of the same sample, or different time points (see kinetic vs replicate). Files may be in tab delimited format with the extension .dat, .txt or .csv or a single Excel sheet in a .xls or .xlsx file.
At this time, Alchromy produces three types of output files:
- A text file (.txt) reporting operating parameters, fit values, and composition percentages.
- An image file (.png) graphing the experimental and fit waves.
- A spreadsheet (.xslx) of the entire fit wave used in the graph.
There are many changes in the works! Below is a list of features already in development.
- Better error handling.
- Improved status reporting in GUI.
Input of multiple waves from a single file (xslx or csv format).Batched deconvolution from GUI, with updating progress bar.More informative output file names.
