Independent Optical Research & Systems Design
Advancing Light Imaging.
Optical Microscopy, Adaptive Optics, Lens Design and Computational Microscopy
Restoring diffraction-limited resolution, translational Raman diagnostics, multiphoton imaging, coherent nonlinear spectroscopy, and lens design.
The Lineup
Our Core Techniques.
Engineered optical systems with their associated research papers, application notes, and foundation theory guides.
Multiphoton Microscopy.
Two-photon excitation fluorescence with ultrafast pulse control.
Deep-tissue nonlinear laser-scanning microscopy with intrinsic 3D sectioning, femtosecond pulse delivery, dispersion compensation (GDD), and holographic wavefront shaping for scattering in vivo media.
Associated Research & Guides
4 publicationsFast Dynamic Wavefront Shaping for Multiphoton Microscopy using Piston-like MEMs
Read article ›Optofluidic Spatial Light Modulator in Multi-Photon Imaging
Read article ›TPEF: Improving Speed and Deep Tissue Imaging by Holography (DASH & PMC)
Read article ›Two-Photon Excitation Fluorescence (2PEF)
Read foundation guide ›Raman Microscopy.
Autofluorescence-free real-time tissue spectroscopy & imaging.
Suppression of biological autofluorescence via compact 1064 nm dispersive fiber-probe Raman spectroscopy and nosepiece-integrated confocal Raman microscopy for real-time surgical tumor margin assessment.
Associated Research & Guides
5 publications1064 nm Fiber Probe Raman Imaging for Human Bladder Resectates
Read article ›Confocal Raman Microscopy with Adaptive Optics
Read article ›Raman Intensity Calibration from 500 to 1100 nm Laser Excitation
Read article ›Raman Wavenumber Calibration by Paracetamol (785 nm)
Read article ›Raman Imaging
Read foundation guide ›Coherent Raman Microscopy.
Video-rate label-free chemical imaging via CARS & SRS.
Synchronized dual-color femtosecond/picosecond pulse trains coherently drive molecular vibrational resonances, amplifying chemical signals by orders of magnitude for high-speed live metabolic imaging.
Associated Research & Guides
1 publicationsPhotothermal Microscopy.
Ultra-sensitive label-free absorption detection via thermal lensing.
Intensity-modulated pump beams locally induce time-varying thermal lenses around non-fluorescent chromophores and nanoparticles, detected with phase-sensitive lock-in probe beam scattering.
Associated Research & Guides
1 publicationsAdaptive Optics.
Restoring diffraction-limited focus in scattering tissue.
Sensorless optical aberration correction leveraging transmissive optofluidic modulators and high-speed piston MEMS to eliminate optical aberrations and deliver up to 3.5× signal boost deep inside organoids and brain tissue.
Associated Research & Guides
4 publicationsFast Dynamic Wavefront Shaping for Multiphoton Microscopy using Piston-like MEMs
Read article ›Confocal Raman Microscopy with Adaptive Optics
Read article ›Optofluidic Spatial Light Modulator in Multi-Photon Imaging
Read article ›TPEF: Improving Speed and Deep Tissue Imaging by Holography (DASH & PMC)
Read article ›Lens Systems Design.
Precision telecentric scan lenses and laser resonator CAD.
Sequential and non-sequential ray tracing, 1064 nm diffraction-limited image-telecentric laser scanning lenses, laser cavity ABCD resonators, and automated DLS merit function optimization in Python.
Associated Research & Guides
2 publicationsComputational Imaging.
Open-source chemometrics, phase retrieval, and AI models.
Parallel hyperspectral image processing, SNIP baseline correction, and Vertex Component Analysis unmixing in SpectraMap, paired with vision-transformer models for automated LaTeX equation recognition.
Associated Research & Guides
4 publicationsSpMap: Hyperspectral Package for Spectroscopists
Read article ›PDF LaTeX Equations to LaTeX Code by Deep Learning (pix2tex)
Read article ›2D Optics: Zemax-Standard Optical Optimization, Laser Resonators & AI Engineering
Read article ›Machine Learning for Hyperspectral Images
Read foundation guide ›Research & Tools
All Articles.
Filter by microscopy technique or browse the full publication archive.
1064 nm Image Telecentric Design: Laser Scanning Lens
An image-telecentric laser scanning lens at 1064 nm: chief rays stay parallel to the optical axis, so the image scale does not change when the sensor moves, with diffraction-limited performance.
Fast Dynamic Wavefront Shaping for Multiphoton Microscopy using Piston-like MEMs
Sensorless phase retrieval leveraging a fast high-resolution MEMS phase-only modulator targeting real-time aberration correction in nonlinear multiphoton microscopy across organoids and brain tissue.
2D Optics: Zemax-Standard Optical Optimization, Laser Resonators & AI Engineering
Desktop optical engineering suite featuring a full Lens Data Editor (LDE), sequential/non-sequential ray tracing, Zemax-standard LM-DLS optimizer, laser cavity stability, 54 Herbert Gross presets, and STEP/DXF CAD export.
Confocal Raman Microscopy with Adaptive Optics
First application of adaptive optics in confocal Raman microscopy: a transmissive optofluidic wavefront shaper on the objective nosepiece corrects sample-induced aberrations, boosting Raman signal up to 3.5x in mouse brain tissue.
1064 nm Fiber Probe Raman Imaging for Human Bladder Resectates
Compact dispersive 1064 nm fiber-probe Raman imaging spectrometer that suppresses biological autofluorescence, discriminates tumor from non-tumor human bladder tissue and characterizes kidney stones.
Optofluidic Spatial Light Modulator in Multi-Photon Imaging
Transmissive, low-loss optofluidic phase modulator for sensorless aberration correction in two-photon excitation fluorescence microscopy.
SpMap: Hyperspectral Package for Spectroscopists
Open-source Python 3 package for hyperspectral images: preprocessing, baseline correction, PCA, clustering and spectral unmixing for Raman, IR and fluorescence data.
Raman Intensity Calibration from 500 to 1100 nm Laser Excitation
Standardized protocol to calibrate the spectral intensity (y-axis) response of Raman spectrometers across visible and NIR excitation wavelengths.
PDF LaTeX Equations to LaTeX Code by Deep Learning (pix2tex)
Convert printed scientific equations from PDF papers into editable LaTeX source code using vision-transformer deep learning.
TPEF: Improving Speed and Deep Tissue Imaging by Holography (DASH & PMC)
Dynamic Adaptive Scattering compensation Holography (DASH) and phase-modulation methods that recover diffraction-limited two-photon focus deep inside turbid tissue.
Raman Wavenumber Calibration by Paracetamol (785 nm)
Wavenumber (x-axis) calibration at 785 nm using paracetamol reference vibrational peaks and polynomial pixel-to-wavenumber fitting.
Raman Imaging
Inelastic light scattering, molecular polarizability, vibrational modes, and how hyperspectral Raman cubes are acquired and unmixed into chemical maps.
Coherent Raman Scattering (CARS / SRS)
Third-order nonlinear susceptibility χ⁽³⁾, coherent driving of molecular vibrations with pump and Stokes ultrafast pulses, and video-rate chemical imaging.
Two-Photon Excitation Fluorescence (2PEF)
Quadratic intensity dependence, intrinsic 3D optical sectioning, NIR scattering reduction, and femtosecond pulse duration requirements.
Photothermal Microscopy
Pump-probe detection of local refractive-index gradients (∂n/∂T) induced by optical absorption in non-fluorescent nanostructures and tissues.
Machine Learning for Hyperspectral Images
Dimensionality reduction (PCA), k-means/hierarchical clustering, NMF/vertex spectral unmixing, and supervised tissue classification.
Juan David Muñoz-Bolaños
Independent Researcher in Biophotonics & Optical Systems
I am an independent researcher and optical systems developer specializing in advanced biophotonics, sensorless adaptive optics, and computational microscopy. My work centers on wavefront shaping with high-speed MEMS and optofluidic modulators, real-time autofluorescence-suppressed Raman spectroscopy, precision telecentric lens design, and open-source scientific computing. I design and build optical instruments from optical physics, ray tracing, and automated optimization to parallel chemometrics and AI models.