What kind of spot detection is best?

[dganguli]

There are two options: 1. Decode each pixel into a corresponding gene, then use a connected components labeler to call spots as contiguous genes of a certain size 2. Find spots, pool the intensity, then decode each spot into a gene.

It should be possible, through simulations, to determine under which SNR noise regimes one method is better than another.

[dganguli]

Can leverage simulation in the notebooks directory:
https://github.com/chanzuckerberg/starfish/blob/master/notebooks/Starfish_simulation.ipynb

[ttung]

Both have been implemented, up to the scientists to figure this out! :)