Search bioRxiv⌕ Search

Biology subjects

Pedersen, S. V.

Publications and source records attributed to Pedersen, S. V..

2 recordsLinked to original sources

Label-free 3-D molecular imaging of living tissues using Raman Spectral Projection Tomography

The ability to image tissues in three-dimensions (3-D) with label-free molecular contrast at mesoscale would be a valuable capability in biology and biomedicine. Here, we introduce Raman spectral projection tomography (RSPT) for volumetric molecular imaging with sub-millimeter spatial resolution. We have developed a RSPT imaging instrument capable of providing 3-D molecular contrast in transparent and semi-transparent samples. A computational pipeline for multivariate reconstruction was established to extract label-free spatial molecular information from Raman projection data. We demonstrate imaging and visualization of phantoms of various complex shapes with label-free molecular contrast. Finally, we apply RSPT as a novel tool for imaging of molecular gradients and extracellular matrix heterogeneities in fixed and live tissue-engineered constructs and explanted native tissues. RSPT imaging opens new possibilities for label-free molecular monitoring of tissues.

bioengineering↗

RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis

Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the ensuing fragmentation and lack of reproducibility of analysis workflows thereof. To address these issues, we introduce RamanSPy, an open-source Python package for Raman spectroscopic research and analysis. RamanSPy provides a comprehensive library of ready-to-use tools for spectroscopic analysis, which streamlines day-to-day tasks, integrative analyses, as well as novel research and algorithmic development. RamanSPy is modular and open source, not tied to a particular technology or data format, and can be readily interfaced with the burgeoning ecosystem for data science, statistical analysis and machine learning in Python.

bioinformatics↗