There are a few different respirometry methods you could follow; it depends what exactly you need from these measurements. Flow-through is typically more expensive but also more stable and reliable than closed box at the scale of an individual fly. In any case it is likely to be relatively expensive to set up, as to achieve good discrimination between treatment groups or individuals, and because the animals output such a small volume of CO2, the CO2 analyser precision must be high. Fortunately, D. melanogaster have a respiratory quotient of ~1 so you do not need to also measure O2 production to accurately calculate metabolic rate. You only need a stable baseline reading and then a measure of CO2 production to estimate metabolic rate at rest, but you might be limited to the higher end of Sable Systems or Li-Cor instruments in order to reliably detect a difference between baseline and animal CO2 rates.

Some examples of Drosophila respirometry:

Berrigan and Partridge (1997) used a flow-through respirometry on individuals using a combination of Sable and Li-Cor instruments.

See: http://www.sciencedirect.com/science/article/pii/S0300962997000303

Promislow and Haselkorn (2002) used a constant volume respirometry system with a multiplexer (Sable) to measure multiple flies at once.

See: http://onlinelibrary.wiley.com/doi/10.1046/j.1474-9728.2002.00009.x/full

I have used a two-channel Li-Cor flow-through respirometry system to measure individual flies, the methods of which are published here:

http://jeb.biologists.org/content/216/17/3350

Hope this helps, and I can try to answer any further questions you may have.

Pieter

Have you come to any conclusion? Have you thought about this "self-built" respirometry analysis?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205100/

Thanks. I'll take a look at this.

For now, my conclusion is that I don't need to do this as urgently as I thought and I'll worry about it if it seems to become important again. But it is a general interest, so it will be good to know how practical it is.