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Topic: DIY chlorophyll a fluorometer build help needed (Read 5783 times) previous topic - next topic


I am very new to Arduino and coding in general but i have a somewhat ambitious project i would like to try out. I would like to build a fluorometer for measuring chlorophyll a fluorescence. This is a tool commonly utilized for measuring certain photosynthetic properties in plants and algae. Basically, it consists of a flash of light from and LED which excites fluorescent photopigments within the plant or algae. The resulting rise in chlorophyll fluorescence is then recorded with a photodiode. A high band pass filter is placed in front of the photodiode so that only the fluorescence signal and not the LED flash itself is detected by the photodiode. 
          As far as hardware goes, i believe i need little more than a good LED capable of very quick flashes of light, a photodiode (im using a very basic one for now and once i have figured out how to run things, i will upgrade to a much better one), and some sort of amplifier as i will ultimately be detecting very low light levels. Ideally i would like to control this device using the Arduino platform (currently i have the UNO but i can get something else if need be) and some graphical user interface. The "product" i would be interested in is both a data plot and a text file of light levels encompassing the flash of light. Depending on what i am interested in, the time scale for the entire thing would be roughly 500ms to several seconds, with samples being recorded at least every millisecond (every 10-100us would be better).
           For the LED, i am using a Cree LED with a buck puck driver which, at least on paper, can provide the pulses of light i need. I have been able to get reasonable 1-10ms flashes of light by controlling it with an Arduino but i would like to get faster flash rates (this may require the use of a large capacitor). I have also been able to log light sensor data in real time using processing and in Matlab. My problem is doing both at the same time and without any sort of delay. In addition, i am not sure what the best software would be in terms of creating a GUI. Matlab and labview are out of the question due to costs. Currently i am thinking MegunoLink or Processing but i am very open to suggestions.
            Basically, i am looking for any general guidance as to the feasibility of this project using the arduino platform and what coding tools/programs are most appropriate to make it happen. A more specific problem i am currently having is how to send data over the serial terminal (light sensor data) while simultaneously sending a signal to the arduino through the serial port to initiate an LED pulse. 
            Any and all guidance/suggestions/questions/comments are welcome as i am very much hoping and in need of some help. Thanks in advance for your time and sorry for the long thread.


      Kenneth D. Hoadley
      Student at University of Delaware


Maybe look at using one of the PWM outputs to drive the LED, while using the same output to 'gate' the photodiode and feeding this in to an integrator, reading the integrator output using an analog input...
So the PWM generates controller length pulses..the LED is lit for that time, and the Photodiode is 'read' at the same time..with the output being integrated over that time.....

Would give you the capability of being able to vary light pulse times.

Next step: Using two synchronized PWM outputs... one to control the LED, another to control the photodiode so you could also measure phosphorescence....



Have you had any luck with the project? I am very interested in this as well, but the only trouble with my application is that I need to be able to record fluorescence measurements of chlorophyll-a from approximately 10 meters away. I was thinking that light pulses from a blue laser could be used in conjunction with a highly focused-lens photodiode with an integrated band pass filter to record the fluorescence response.

Can anyone provide any suggestions as to how I might build this???




Feb 15, 2014, 06:05 pm Last Edit: Feb 15, 2014, 06:08 pm by drbrian Reason: 1
Sounds like a good idea, just want to get access to cheap bandpass filters. In uk, knightoptics does 11mm filters that would be good. for £30ish + vat AND DELIVERY.
Another place to start an enquiry would be  http://publiclab.org/wiki/chlorophyll-fluorometer (just set up)


Hi all,

Interesting concept. I'm a student in Oceanography and i'm planning to write my thesis on airborne remote sensing of waterbodies. It  will be a feasibility study on low-cost (diy) methods for spatial monitoring of algae/cyano blooms using UAVs in combination with consumer camera's. So I am really curious on your progress regarding diy (remote) fluorescence measurements.

Does anyone have some thoughts on using CCD/CMOS cameras and band pass filters to measure absorption of pigments of algae and cyano's? 

Hope to hear from you guys.


I am working on a very similar project. I have found this paper very informative, but I am new to arduino as well, and haven't started writing code yet.

In situ Measurements of Phytoplankton Fluorescence Using Low Cost Electronics
Thomas Leeuw,* Emmanuel S. Boss, and Dana L. Wright
Sensors (Basel). 2013 Jun; 13(6): 7872-7883.
Published online 2013 Jun 19. doi:  10.3390/s130607872

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