George Emanuel

I like the approach overall of coming up with new metrics to distinguish between correctly and incorrectly called barcodes. I have a few comments that I hope can help as...

This error arises because it's unable to find a threshold that achieves the desired misidentification rate. This could be because there are few blanks or few decoded barcodes so that...

This is a warning coming from the Decode task, but the cases when this warning arises are handled in lines 115-127 of registration.py, so there is nothing you have to...

That is a warning that arises because there are bins in the histogram that contain no barcodes resulting in division be 0. The error doesn't alarm me, but I expect...

Typically we spots visible over the background through the experiment I find that I can get something to decode. How far is your decoding going? With the warnings you've shown,...

The intensity vs area plot doesn't look promising. If this is a measurement with ~16-20 bits then I would expect to see a better defined higher intensity population. I'd suggest...

Having small regions where the camera was saturated should not cause significant problems. For a 16 bit measurement in U2OS cells I am surprised there are SNR concerns, especially if...

I agree that your image looks like it has low SNR and it is unclear that the spots we do see in your image are true spots rather than stray...

Ideally the whole decoding process would be computationally efficient enough to run on a single modest workstation computer within 3-6 hours. It's somewhat difficult to fit more than ~100 cores...

Ideally a 22 bit dataset with 2500 FOVs each 2048x2408 pixels and 7 z planes could be decoded in 3-6 hours. This would cover a typical experiment of 1 square...