Welcome! You've found the repository for rainbow 🌈 -- a napari plugin for inspecting and unmixing spectral images. This project is in pre-alpha, so expect some glitches. Current functionality includes the ability to inspect pixel spectra and perform linear unmixing.
You can install rainbow via pip:
pip install napari-rainbow
At the moment, rainbow contains an inspector widget for viewing pixel spectra and an unmixing widget for performing linear unmixing. Here's a quick introduction to each of these components.
To view the spectra that make up your spectral image, select the Inspect widget from the rainbow dropdown menu. The widget will plot a live readout of the pixel spectra as you move your cursor over the image.
The normalization setting allows you to easily view and compare signals of different intensities.
To determine the amount of fluorescent label that exists within your spectral image, we can perform unmixing using the nonnegative least squares algorithm. This process requires that you have an endmember CSV file corresponding to the fluorophores used to label your sample. You can create this endmember file yourself or generate one from FPbase. Note that the wavelength range of your endmembers must match that of your spectral image.
To perform unmixing, first open your spectral image. Then open the Metadata widget to identify which dimension corresponds to your spectral information. Next, open the Unmix widget and click the import button. The importer only accepts CSV files representing your endmembers. If your CSV file is formatted properly, you will see the endmember spectra plotted for you to review. When you are ready, click unmix to start the nonnegative least squares algorithm. The spectral image will be replaced by the unmixed channel image.
Distributed under the terms of the BSD-3 license, "rainbow" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.