|MadSci Network: Microbiology|
It's not completely clear exactly how you're growing your algae nor what type(s) of algae you're using, but I'll make a few assumptions & tell you what I can.
Since you're using a spectrophotometer, I'll assume you're growing them under somewhat std. liquid culture conditions. My only experience w/ algae was work w/ blue-green algae/cyanobacteria for my thesis/post-doctoral research many moons ago. For our liquid cultures, we used turbidimetric light-scattering to measure their optical density in the same manner that bacterial culture optical densities are determined. In this case, light absorbance by chlorophyll & other pigments is ignored. However, the wavelength used for determining culture optical densities must be adjusted to avoid any pigment absorbance while remaining suitable for measuring light-scattering by the algae. For the blue-greens, we used 550 nm, slightly shorter than the 650 nm typically used for non-absorbent bacterial cultures.
If you're studying eukaryotic algae, they'd be considerably larger than the blue-greens & their pigment absorbance spectrum may differ somewhat. But I would think you could use the same principles that were applied to the blue-greens to find a suitable wavelength for determining their optical densities, as well.
In summary, I would recommend avoiding any method that depends on pigment analysis. If spectrophotometry doesn't work out, you might even be able to plate the algae out on solid culture media & count colonies. It would be much more laborious & may not even be feasible for some algae. But it would be another approach for directly measuring cell numbers/biomass in the liquid cultures.
Best of luck w/ your studies & I hope this advice is helpful,
Jeff Buzby, Ph.D.
CHOC Research Institute
Try the links in the MadSci Library for more information on Microbiology.