Excalibur Mineral Corp - Raman Microscope Rebuild Project



Overview
Olympus BX41 Microscope
Photos
More photos
The motor controllers
Spectrum processing
Testing the spectrograph
Notch filter Alignment
More Reference Photos
Oscilloscope photos
Filter tests
#0 - Neon
#1 - Crocoite
Early User Interface
Reverse Engineering
Strip Chart
Wavelength & Wavenumber Calibration
Peak labeling
Database Matching
More Filter Tests
Alignment
Python Application
#2 - Lopezite (potassium dichromate)
#3 - Sulphur
Labram - first Raman spectra
Beam settings
#4 - Realgar
Alignment Tool
Thermo-Electric Cooling
3D printed parts
Faulhaber motor
473nm "BioPhotonic Scanner" (for parts)
uScope Head Problems
Scalloping / Sawtooth patterns
CCD focus
Peak Ringing
#5 Fluorapatite
#6 Orpiment
#7 Pararealgar
The Corundum Conundrum
Destructive Testing
Calcite
Dark Frame Sub and CCD flush
CCD driver MCU firmware and timing
Anti-Stokes Region and Raman Cooling
Larger CCD
ADC - signal conditioner
CCD controller
20181111 Recent Scans
OH band
para-dichlorobenzene
Mayhew 16-bit ADC
CrPb minerals
Ibuprofen
Forsterite
Area Scans (Full Frame Transfers)
natrolite
eudialyte
ibuprofen2
Audible Mineral Vibrational Spectra
532nm laser 20mW
532nm laser 200mW
Oblique vs. Rectilinear Laser Injection
Virtual Spectrograph Slit
Objective Alignment
Peak Redshifts
Sidebands
Quantum Illumination
Soft Modes
Current Version
To Do


In a Nutshell

A laser strikes a sample and most of its light is reflected without being changed. That unchanged light is filtered out as much as possible. The small amount of light that has been changed and reflected by the sample contains information about the sample. That small amount of changed light is sent into a spectrograph which does the same thing that a prism does. But instead of a big colorful rainbow, a smaller range of wavelengths are seen that are relatively close to the laser's own wavelength. (which is why the unchanged laser light has to be filtered out so that we are not blinded by it. It is similar to what astronomers do to see distant planets orbiting around bright stars. Astronomers block out the bright starlight in order to see the faint light reflected off the distant planets.) The spectrograph produces a spectrum which shows discrete peaks. That is the Raman spectrum and deciphering it reveals a lot of information about the sample.

Overview

The parts of a Horiba Aramis Labram Raman microscope were being sold piecemeal locally by a industrial salvage dealer at reasonable prices. Unfortunately we did not obtain the original detector, and some of the optics, but most of the essentials were there. So we decided to try and rebuild it. At that time (2016?), Raman spectrographs were big, expensive, and apparently high-maintenance. Nowadays (2025) they are small, way more powerful, and ubiqitous. And Raman spectra databases are growing in number. The columns above are roughly ordered by progress over time, the maintenance became too time consuming, and many problems remain unresolved. And we never got around to exploring many ideas like using a PEM to modulate laser polarization or looking for interesting effects like soft modes in quartz alpha-beta transitions (don't we need an oven for that?)

General

Raman Spectroscopy deals with molecular-scale properties. It reveals information about both chemistry and structure. It has a sort of blindspot: it provides information that is complementary to that of IR spectroscopy. It is a really fun area to study. Not quite as complicated as sub-atomic and sub-nuclear. But complex enough to require deep thinking.

Theoretically

The Raman spectra can be 'ab initio' synthesized in terms of Density Functional Theory (to some extent?). A group theoretic analysis of known molecular symmetries can be used to derive the selection rules that determine whether or not an expected peak will be physically detectable ("not forbidden") for a given method of observation.

Physically

The Raman spectrograph detects certain excitable modes (thermal lattice vibrations etc); the inelastic (energy exchanging) deformations of molecular structures. The induced excitations allows the Raman Effect to be used for "Raman Cooling" in the case of anti-Stokes scattering. The Raman effect is also used as a gain medium in Raman Lasers of arbitrary wavelengths which is very interesting. Also, the ability to measure the rotational spectra of gases looks treatable mathematically identically to that of double sideband suppressed carrier frequency modulated spectra where the (small, gaseous) molecules are spinning around like tiny satellites in space. Supposedly you can get such rotational spectra from non-gaseous materials like camphor.

Technology

The Horiba Aramis Labram Raman microscope uses holographic notch filters to remove the Rayleigh (elastic) scattered light from the beam before it reaches the spectrograph. This type of notch filter (as opposed to dilectric types) have certain benefits, but they seem to be constructed from a photographic gel which can degenerate over time requiring angular adjustment of the filter. Some Raman filters are also designed to simultaneously act as beamsplitters, AKA "injection/rejection" filters which can become very difficult to align. A more discrete solution is to use a separate dichroic beamsplitter with some loss of sensitivity. More recent spectrographs seem to be using transmission gratings. Recent spectrographs also seem to have better performance below 100/cm. More recent developements show considerable progress which marks the start of a golden age for photonics and its use for materials analysis. Polarization is big deal in Raman spectroscopy. If the exciting laser is linear polarized it will have a strong effect on certain specimen directions a weaker effect on the others. For this reason circular polarizers, PEMs, or non-polarized lasers can be used to give an average Raman response for a single specimen orientation. Or the specimen can be mounted on a rotating stage. Or the specimen can be powdered into averaged orientations (as in powder x-ray diffraction for the same reason). But a linear polarized exciting laser gives valuable structural information when the specimen is in a well-known orientation. The ratio of intensities for different polarization is an important figure (Raman Tensor). Polarization can be difficult to control in the optical beam path to the specimen, and I suspect its path to the detector may be important as well.

User Interface

The Raman spectra peaks represent vibrational mode energy transitions. The vibrational modes are associated with atomic bonds in the molecules. The peaks on the high-shift end of the Stokes side represent modes in the bonds of lighter elements because those peaks have longer wavelengths (higher wavenumber shifts) and represent lower (red-shifted) Raman scattered photon energies meaning the exciting laser's photons have lost a lot of energy to the specimen (because the lighter elements have less inertia). Pfew! The peaks closer to the laser line on the Stokes side represent the modes of bonds between heavier atoms. Generally the anti-Stokes lines are supposed to be symmetric with the Stokes side- but their transitions are less favorable because the anti-Stokes transitions involve removing heat from the specimens and efficient cooling is contrary to the second law of thermodynamics. The peak positions are generally characteristic of chemical and structural properties. But an individual peak can move around in a still background of the other peaks if the molecular structure of a specimen is stressed in a particular bond-dependent direction. In the context of Raman spectroscopy, 'temperature' becomes a more interesting topic in terms of thermal phonons when treated as quasi-particles that carry momentum as quantized sound waves.
Partial Specs: Horiba LabRAM Aramis (modified by our rebuild) CCD Hamamatsu C7041 single stage TEC head with S7031-1006S back-thinned FFT-CCD sensor with AR coated sapphire window (beware of Cr fluorescence). Pixels: 1044x64. Active pixels: 1024x58. Pixel size 24x24um. Spectral range 200-1100nm. Gratings 600, 950, 1800 Microscope: Olympus BX41 Objectives U-P4RE turret Olympus epi-illumination alignment objective Olympus 10x CY PLAN N (filter removed) NA0.25 inf/- Olympus 40x PLAN inf/0.17 NA 0.65 Olympus 50x UIS2 MPLAN inf/- NA 0.75 Olympus 100x UIS2 MPLAN inf/- NA 0.9 stage U-SP fixed stage binoc head U-BI30 WF10X eyepieces turrets: U-P4RE with objective centering U-D5DREMEC motorized turret condensor fiber optic illumination (Russian-made fiber light source) 632.8nm 20mW TEM00 LP HeNe Meredith Instruments Laser: beam diameter: 0.80mm divergence: 1mRad head: 660x44.5mm (h*c/633nm)*(6.242E+18)=1.95929515 eV/photon 473nm "10W" blue diode laser: B&W BWB-10-OEM ; not currently used 532nm 200mW Melles-Griot green diode laser. PC Dell running Win XP Python 2.7 (3.x ready?) numpy scipy mathplotlib PIL pyserial others Arduino IDE Chipkit Libraries MCUs Arduino Mega32 Digilent Chipkit uc32 (alt. Max32 for full frame transfers) Adafruit Motor Shields v2.3 ADCs Mayhew 16-bit extended ADC shields

Reduce a fraction

 
Numerator
Denominator

Convert to Wavenumber

 
Laser (nm)
Wavelength (nm)

Convert to wavelength

 
Laser (nm)
Raman shift (cm^1)

Min Spot Size (nm)

 
Laser (nm)
NA

Min Spatial Resolution (nm)

 
Laser (nm)
NA

Rruff Stuff


American Mineralogist Crystal Structure Database:

Mineral
Author
Chemistry Search
Cell Parameters and Symmetry
Diffraction Search
General Search
Search Tips

Logic interface AND OR
Viewing (About File Formats) amc long form amc short form cif
Download amc cif diffraction data



Misc References:

Raman paper, 1928
Raman's Nobel lecture 1930
C. V. Raman and the Discovery of the Raman Effect
Raman Scattering

Labram Aramis Brochure
Labram Brochure
Labram Aramis Specs
LabSpec5 Manual (.pdf 4MB)
Stark effect
Lamb shift

Raman bands explained
Brillouin Scattering

One reason why wavenumbers are not in units of 'K' Kaysers (NIST)
"We note that the basic unit of temperature, the kelvin, is equivalent to about 0.7 cm-1, i.e., the value of the Boltzmann constant k expressed in wavenumber units per kelvin is 0.695 035 6(12) cm-1/K. One reason for citing this particular equivalency involving the internationally accepted symbol for the kelvin (K) [1] is to suggest that use of the letter K as a symbol for 1 cm-1 (1 kayser) should be discontinued."
At this time I prefer using "/cm" rather than "cm^-1". Note: the Raman wavenumber shift is relative to the excitation energy which differs from its meaning elsewhere.

Broadband Raman spectrometer for single-wall carbon nanotubes
Impact of Volume Phase Holographic on Raman Instrumentation
Filter Spectra at Non-normal Angles of Incidence
Molecular Vibration
Normal Mode
Crystallographic Point Group
Symmetry Selection Rules
Character Table
Mulliken Symbols
Schonflies Notation
List of character tables for chemically important 3D point groups
Group Theory and Vibrational Spectroscopy
Lecture5 - Light coupling and selection rules
Atomic Structure - Condon and Odabasi
Understanding Character Tables of Symmetry Groups
A Pragmatic Introduction to Signal Processing
Raman Scattering in Crystals
Introduction to Interpretation of Raman Spectra Using Database Searching and Functional Group Detection and Identification

Books etc.:
Group theory and symmetry in chemistry - Lowell H. Hall
Feynman Lectures on Physics
The Science of Radio - Nahin
Physical Chemistry - Atkins, De Paula
Mathematical Elements for Computer Graphics (1976) - Rogers, Adams
Quantum Interference between Light Sources Separated by 150 Million Kilometers (2019) - Deng et al
Astrophysical Concepts - Harwit
Probability and Information Theory with Applications to Rada - Woodward
Waveforms - Tilton
Light in Flight - Abramson

Horiba:
The Optics of Spectroscopy by J.M. Lerner and A. Thevenon
The Correlation Method for the Determination of Spectroscopically Active Vibrational Modes in Crystals
(organic) Raman Bands
Raman Spectroscopy for Geological Materials Analysis
Raman Polarization Measurements: Keeping Track of the Instrumental Components Behavior
Why Are the Raman Spectra of Crystalline and Amorphous Solids Different?
Entrance Optics
The Optics of Spectroscopy
Fran Adar

Raman Data Search and Storage (RDSS) software
WURM a database of computed physical properties of minerals
Theoretical modelling of Raman spectra(pdf)
ABINIT software source code
American Mineralogist Crystal Structure Database
Zipped RRUFF Data (add to CrystalSleuth's db)
Highlights in Mineralogical Crystallography
MEMS diffraction gratings
GeoRaman
Raman Data Analysis
Dual Readout
Frame Transfer Cameras
Relative Intensity Correction of Raman Spectrometers: NIST SRMs 2241 Through 2243 for 785 nm, 532 nm, and 488 nm/514.5 nm Excitation
Procedures for Wavelength Calibration and Spectral Response Correction of CCD Array Spectrometers (calibration of spliced spectra)
Stitched Scan Spectrograph
Ghostbusting - Spectres in Spectra (Residual Bulk Image)
What is Residual Bulk Image and how do to deal with it
FITS Liberator
FITSworks
Free-space vs. Fiber coupling
Mirror vs. Lens spectrographs

Intro to Raman Spectroscopy 1
Intro to Raman Spectroscopy 2
Intro to Raman Spectroscopy 3
Intro to Raman Spectroscopy 5
Intro to Raman Spectroscopy 6
Intro to Raman Spectroscopy 7
Intro to Raman Spectroscopy 8

Condenser
Collimator (the output aperature is same size as the output beam-width at infinity focus)
Telecentric
Infinity Correction
Getting light into a monochromator

CVI dichroic beamsplitters

The Effect of Microscope Objectives on the Raman Spectra of Crystals
Microscope objectives with NA>0 are not epi-telecentric...

Centroid of a Peak

Handbook of Minerals Raman Spectra
Intro to Cryst. Sym. and Raman Spect.
SERS handbook

Motional Quantum Ground State of a Levitated Nanoparticle from Room Temperature
Alian Wang et al:
Development of the Mars microbeam Raman spectrometer (MMRS)
Stand off ultra-compact u-Raman sensor for planetary surface explorations
Understanding the Application of Raman Spectroscopy to the Detection of Traces of Life
Procedures for Wavelength Calibration and Spectral Response Correction of CCD Array Spectrometers (calibration of spliced spectra)
Autonomous soil analysis by the Mars Micro-beam Raman Spectrometer (MMRS) on-board a rover in the Atacama Desert: a terrestrial test for planetary exploration

Other experiments involving eclipses:
Synopsis: Blocking out Starlight
 Vortex coronagraph
 Coronagraphic Notch Filters for Raman Spectroscopy(NASA)
 Demonstration of tunable optical notch filter using 1D opto-VSLI processor
 Topological quantum number
Testing General Relativity
 My Do-It-Yourself Relativity Test

DIY Raman projects:
jm-derochette.be - Raman Microscopy for the Amateur Mineralogist
adolph cortel - Use a piece of cardboard as a Raman filter
Charles LeLosq's RamPy (geoscience source code)
Arbildo Lopez Aurelio
erossel - DIY Raman spectroscopy
radagast - Lego Raman
flatcat- RamanPi
Technologia Incognita
Hanson and Vargis

Videos:
Horiba Operation - South Dakota State University
Renishaw Operation - MDITR
Tips for Laser Alignment - CO2 cutter/engraver


Simulating an Optics bench using "Povray" software


Old version of Povray. The doublet is composed of flint and crown glass. Their different indices of refraction are simulated in POVray; but not dispersion. I also wasn't able to get and older version of "Blender" to be useful as an optics simulator.

     

The Pacman sound made by the extended range scanning stepper motor.


Disclaimer: The information on this webpage is provided for educational purposes only
and no claims are made of accuracy, or suitability for any particular use by the reader.

Excalibur Mineral Corp 2015-2025