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 fluorescence microscopy, coherent nonlinear spectroscopy, and lens design.
Latest Dispatches.
Newest optical simulations, instruments, and analysis articles.
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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.
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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.
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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.
Multiphoton Fluorescence Microscopy.
Multiphoton excitation fluorescence with ultrafast pulse & wavefront control.
Deep-tissue nonlinear laser-scanning fluorescence microscopy with intrinsic 3D sectioning, femtosecond pulse delivery, dispersion compensation (GDD), and holographic wavefront shaping for scattering in vivo media.
Related Papers & Foundations
4 items
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Fast Dynamic Wavefront Shaping for Multiphoton Microscopy using Piston-like MEMs
Read paper ›
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Optofluidic Spatial Light Modulator in Multi-Photon Imaging
Read paper ›
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TPEF: Improving Speed and Deep Tissue Imaging by Holography (DASH & PMC)
Read paper ›
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Multiphoton Fluorescence Microscopy
Read foundation ›Raman & Coherent Raman Imaging.
Autofluorescence-free 1064 nm & confocal Raman with video-rate CARS & SRS.
Suppression of biological autofluorescence via 1064 nm dispersive fiber-probe and nosepiece-AO confocal Raman spectroscopy, unified with synchronized ultrafast pump-Stokes coherent Raman imaging (CARS & SRS) driving χ⁽³⁾ molecular vibrations.
Related Papers & Foundations
6 items
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1064 nm Fiber Probe Raman Imaging for Human Bladder Resectates
Read paper ›
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Confocal Raman Microscopy with Adaptive Optics
Read paper ›
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Raman Intensity Calibration from 500 to 1100 nm Laser Excitation
Read paper ›
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Raman Wavenumber Calibration by Paracetamol (785 nm)
Read paper ›
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Raman Imaging
Read foundation ›
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Coherent Raman Imaging
Read foundation ›Photothermal 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.
Related Papers & Foundations
1 itemsAdaptive Optics & Computational Imaging.
Sensorless wavefront correction, hyperspectral unmixing, and deep learning.
Sensorless aberration correction with transmissive optofluidic modulators and high-speed piston MEMS (up to 3.5× deep-tissue signal boost), combined with parallel hyperspectral chemometrics (SpectraMap PCA/VCA) and vision-transformer AI.
Related Papers & Foundations
7 items
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Fast Dynamic Wavefront Shaping for Multiphoton Microscopy using Piston-like MEMs
Read paper ›
⤢
Confocal Raman Microscopy with Adaptive Optics
Read paper ›
⤢
Optofluidic Spatial Light Modulator in Multi-Photon Imaging
Read paper ›
⤢
TPEF: Improving Speed and Deep Tissue Imaging by Holography (DASH & PMC)
Read paper ›
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SpMap: Hyperspectral Package for Spectroscopists
Read paper ›
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PDF LaTeX Equations to LaTeX Code by Deep Learning (pix2tex)
Read paper ›
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Machine Learning for Hyperspectral Images
Read foundation ›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.
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Raman Imaging
Inelastic light scattering, molecular polarizability, vibrational modes, and how hyperspectral Raman cubes are acquired and unmixed into chemical maps.
Read Foundation ›
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Coherent Raman Imaging
Third-order nonlinear susceptibility χ⁽³⁾, coherent driving of molecular vibrations with pump and Stokes ultrafast pulses, and video-rate chemical imaging.
Read Foundation ›
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Multiphoton Fluorescence Microscopy
Nonlinear n-photon absorption (I² / I³), intrinsic 3D optical sectioning, NIR scattering reduction, and femtosecond pulse dispersion requirements.
Read Foundation ›
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Photothermal Microscopy
Pump-probe detection of local refractive-index gradients (∂n/∂T) induced by optical absorption in non-fluorescent nanostructures and tissues.
Read Foundation ›
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Machine Learning for Hyperspectral Images
Dimensionality reduction (PCA), k-means/hierarchical clustering, NMF/vertex spectral unmixing, and supervised tissue classification.
Read Foundation ›
⤢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 Imaging
Third-order nonlinear susceptibility χ⁽³⁾, coherent driving of molecular vibrations with pump and Stokes ultrafast pulses, and video-rate chemical imaging.
⤢
Multiphoton Fluorescence Microscopy
Nonlinear n-photon absorption (I² / I³), intrinsic 3D optical sectioning, NIR scattering reduction, and femtosecond pulse dispersion 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.