SLSonji Lamichhane

02 / Research

Analytical workflows for living systems.

01

Raman spectroscopy & chemometric modeling

Quantitative cell phenotyping workflows for reproducible spectral acquisition and interpretation.
  • Optimized cell seeding density and membrane-supported culture conditions for reliable single-cell occupancy and Raman acquisition.
  • Used Raman spectroscopy and chemometric analysis to evaluate substrate compatibility and distinguish cell phenotypes by their spectral signatures.
  • Applied MATLAB and Eigenvector PLS Toolbox for spectral preprocessing, PCA/PLS modeling, outlier detection and model evaluation.
  • Developed PLS-DA models from Raman spectra of 200+ cells, achieving more than 93.5% classification accuracy across hydrogel stiffness conditions.
  • Evaluated model transferability using 1,000+ Raman spectra across datasets and experimental conditions.
02

Hydrogel micro-well platforms

A noninvasive, Raman-compatible platform for single-cell analysis and longitudinal tracking of non-adherent cells.
  • Designed silicon micropillar stamps using KLayout, photolithography and dry etching to produce hydrogel microwells with integrated alphanumeric fiducial markers.
  • Developed micro-embossed hydrogel workflows, tuning composition, embossing time and processing conditions to control geometry and mechanical properties.
  • Characterized hydrogel stiffness with nanoindentation and well dimensions with optical profilometry and AFM.
  • Fabricated Raman-compatible substrates through thin-film deposition and characterized film thickness with an M-probe.
03

Fluorescence tools for living algae

Protein and lipid characterization in Phaeodactylum tricornutum under axenic and bacterial co-culture conditions.
  • Developed a genetic expression and fluorescence-based assay to visualize protein distribution in living algae following bacterial interactions.
  • Engineered Phaeodactylum tricornutum to express SNAP-tag and HaloTag self-labeling fusion proteins using plasmid construction, Gibson Assembly and conjugation.
  • Identified cell-wall-permeable fluorescent dyes with minimal native-fluorescence interference and optimized protein- and lipid-labeling conditions with DOE studies.
  • Verified protein expression and labeling specificity with SDS-PAGE and Western blotting and collaborated with Lawrence Livermore National Laboratory on quantitative NanoSIMS image analysis.