skew-biology

Software for my DIY spectrometers, sensors, pcr, and incubators.

Spectrometer Software

Software for reading a spectrum from a DIY spectrometer using OpenCV,
calibrating it using non-linear regression to the function with the gnu scientific library.

Example DIY Lego Spectrometer

• 1k diffraction grating
• Sony IMX179 8MP CCD
• Velcro, aluminum foil, and a lot of black legos
• CCD at m=0

Usage:

spec [roi x y w h] [cal C0 C1 C2]

The ROI and constants for calibration can be specified on the command line. The calculated intensity and wavelength can be saved to csv alongside the calibration file for analysis in other programs.

Calibration Details

This software currently uses a second-order polynomial for calibration off a minimum of three points. There may be value in moving to a cubic function.

nm = C0 + C1p + C2p^2

Calibration References

• Calibrating the Wavelength of Your Spectrometer
• OceanOptics Cubic Calibration
• PublicLab Linear Calibration

Selecting a Region of Interest

On startup the region of interest can be selected with a mouse. The pixels in this region of interest are summed to calculate intensity.

Commands:

Command	Note
top	lists the top wavelengths, intensities, and pixel indicies
cal	enters calibration mode
save	saves to csv along with the calibration

Building:

cmake .
make

Example usage:

Calibrating a CFL using the mercury peaks terbium peaks. Appears to accurately predict europium peaks at 612nm.
CFL Spectrum Reference

Incubator

PID controled incubator w/ IR

RGB

simple rgb sensor control for recording the rgb values of a sample
being incubated by a connected computer