Pipeline for the removal of hardware related artifacts and background noise for Raman spectroscopy.

Raman spectroscopy is a real-time, non-contact, and non-destructive technique able to obtain information about the composition of materials, chemicals, and mixtures. It uses the energy transfer properties of molecules to detect the composition of matter. Raman spectroscopy is mainly used in the chemical field because background fluorescence and instrumental noise affect biological ( and ) measurements. In this method, we describe how hardware related artifacts and fluorescence background can be corrected without affecting signal of the measurement. First, we applied manual correction for cosmic ray spikes, followed by automated correction to reduce fluorescence and hardware related artifacts based on a partial 5 degree polynomial fitting and Tophat correction. Along with this manuscript we provide a MatLab script for the automated correction of Raman spectra.•"" offers an automated method for the removal of hardware related artifacts and fluorescence signals in Raman spectra.•"" provides a modifiable MatLab file adjustable for multipurpose spectroscopy analysis.•We offer a standardized method for Raman spectra processing suitable for biological and chemical applications for modular confocal Raman spectroscopes.