ramanspy.preprocessing.protocols.bergholt2016

ramanspy.preprocessing.protocols.bergholt2016() → Pipeline

A basic preprocessing protocol approximating the one adopted in Bergholt MS et al. (2016) [1].

Consists of the following steps:

• baseline correction with polynomial fitting of order 2 in the range 700-3600 cm-1;

• spectral cropping to the fingerprint region (700-1800 cm-1);

• (Unit) Vector normalisation (pixelwise).

• cosmic ray removal with Whitaker-Hayes algorithm.

References

[1]

Bergholt MS, St-Pierre JP, Offeddu GS, Parmar PA, Albro MB, Puetzer JL, Oyen ML, Stevens MM. Raman spectroscopy reveals new insights into the zonal organization of native and tissue-engineered articular cartilage. ACS central science. 2016 Dec 28;2(12):885-95.

Example

pipeline = preprocessing.protocols.ARTICULAR_CARTILAGE()
preprocessed_data = pipeline.apply(data)