Increase speed of spot detection

[jstitlow]

Compute time on our HPC ranges from 1-30 minutes, depending on the number of spots.

Any general advice on how to speed this up? I've split up the analysis using the multiprocessing module, but returns are rather limited.

Is there GPU implementation for bigfish?

Data and computer specs
2047x2047x20 px
100-10000 spots per image
(Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz) x 30 processors
115GB RAM

Also opening a separate issue to discuss the possibility of analyzing images by cell instead of whole frame, and analyzing super-expressing cells in analogue mode (or ignoring these cells to process separately).

Cheers,
Josh

[muellerflorian]

Dear Josh,

30 minutes for an image sounds very long (especially on the type of machine you are using).

could you maybe provide us with an image that takes so longer ([email protected]). then we could so some benchmarking trying to figure out what takes that long ...

what exactly is involved in this analysis?

best
F