For lab scale, lyophilise algae or use conventional pestle mortar to make powder of dried algae biomass and extract using try Bligh & Dyer method using Chloroform:Methanol in 1:1 or 1:2 depending upon the strains followed by separation using NaCl solution. A minimum of two extractions should be sufficient to extract lipids.

I could not speak about polar metabolites, but to estimate total lipid content in algae we used Accelerated Solvent Extraction with hexane

Optimization of an Analytical Procedure for Extraction

of Lipids from Microalgae

Article Optimization of an Analytical Procedure for Extraction of Li...

... and after evaporation of hexane ASE extracts, total extractable lipid content was determined isoperimetricaly . May be it was not most optimised approach, but it did served the purpose of comparison total residual lipid content in different algal species.

I have attached (above and below) couple of publications, which might be helpful.

Optimalization of Extraction Conditions for Increasing Microalgal Lipid Yield by Using Accelerated Solvent Extraction Method (ASE) Based on the Orthogonal Array Design

Dear Tanya, polar lipids and, especially, high polar lipids like SGDGs, could not be extracted by n-hexane...so Folch or B&D protocols are still the most effective, convenient and reliable methods..

Anyway, if we want to compare their effectiveness, we should analyse lipid content in our samples after extraction. I think that saponification in presence of heptadecanoic acid as an internal standart is a good approach to examine it.