Are you looking for a method where you can use low biomass to extract lipid? Is that your question?

Yes, I would prefer a method where I can use lesser amount of biomass to estimate total lipids from cyanobacterial cultures

You can use semiquantitative methods like meauring flueroscense of BODIPY dye technique. Or for gravimetric methods also you can use around 100mg biomass. But you have to perform extraction and measurments with prescision. I hope you are using some cell disruption technique. From my experiance I would recommend sonication for small amount of biomass. 

Thanks Abhishek for your suggestions. But if I take just 100mg biomass, how will I be able to get accurate weight reading? I am planning to use a sonicator for cell lysis.

100 mg is sufficient for gravimetric estimation. In my experience, lesser the biomass more is accuracy, but you need to use small glass vials and if possible freeze dry cells as than it would be easy to handle while weighing the biomass. And do repeat extractions, atleast twice.

Thanks Simrat. But, if we take 100mg of biomass, the amount remaining at the very end would be far less, right? Then, how can we get accurate readings. How accurately can your weigh balance weigh?

Weighing balance that can weigh minimum 10 mg should be fine. If you do the extraction in a preweighed small vial (which protocol do you follow?) and evaporate solvent to weigh the vial again with lipids. If its 10% than you should be good to weigh that amount in precision balance. Keep 4-5 replicates.